Universes Collide
by general MB
Summary: The Master Chief and Cortana have been drifting through space for years, but when they are picked up by a mysterious ship, a new fight begins. Halo crossover story, read to find out who with - rewritten with extended and deleted scenes.
1. prologue

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**Hello, just so you know this is my first story so please feel free to comment**

* * *

Disclaimer: I don't own halo or any other TV show or book mentioned in this story

**Prologue: finish the fight**

There were explosions coming from all over the place as the chief gunned the warthog's engine, trying to get over the jump and into the hangar of the frigate. The Arbiter was manning the hog's machine gun try to take out sentinels in pursuit of the pair, and there was Cortana an AI interfaced with the master chief's suit. She was telling the chief the halo's final firing sequence was starting and they had a few minutes left. That was all he would need as the warthog when screaming off the ramp and into the hangar of the UNSC frigate _forward unto dawn__**,**_ the hog landed and flipped over spilling its occupants on the deck of the hangar. The chief slowly got up as did the arbiter, but the ship was rocked to one side and a tank stored at the other end of the hangar came loose and started heading for The Arbiter. He dived behind some crates just as the tank hit the chief ran toward a computer panel in the hangar. As the arbiter got up the chief looked at him and nodded and he did the same knowing what they had to do. The chief turned to the panel and inserted the chip from his helmet into the console then Cortana's blue holographic form appeared and she said to him.

"Hang on"

She engaged the frigate's engines and they escaped the halo's atmosphere. The chief struggled to hold on but was nearly knocked out of the ship by a flying warthog. He managed to grab hold just as the tank nearly hit him as it was sucked out of the ship. The chief herd Cortana call out to him so he slowly made his way to the console, removed Cortana's chip and reinserted into his suit.

"If we don't make it" she started.

"We'll make it" the Chief reassured.

"It's been an honor serving with you, John"

Then the light from the detonation enveloped the hangar just as the ship entered the portal.

--

"Chief, chief can you hear me?" Cortana cried

The chief felt groggy and then he noticed he was weightless; he flipped on his suit lights to find himself in one of the dawn's corridors. He scooped up his assault rifle and he slowly made his way toward a breach in the hull.

"At last, I thought I lost you too"

"What happened?"

"I'm not sure… when halo fired it shook itself to pieces, did a number on the ark. We made it through the portal just as it collapsed… well some of us made it" Cortana said.

The chief looked out to see the forward half of the dawn was missing; he slowly made his way to the cryo chamber knowing it was his only option for survival.

"But you did it… Truth and the covenant, the flood its finished" Cortana said as the chief inserted her chip into a holo pad near a cryo tube.

"It's finished" The chief said as he floated toward a locker where he deposited his assault rifle and then got into the cryo tube.

Cortana turned to him "I'll drop a beacon but it will be a while before anyone finds us years even… I'll miss you".

The chief looked at her as the lid was closing and said.

"Wake me when you need me".


	2. chapter 1: just another day at work

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 1: just another day at the office**

Captain Marc Anderson sat in his ready room, a man in his early thirties with dark brown hair. He was reflecting on the past few months; how he got assigned to his ship, USS_ Gettysburg, _a sovereign class ship no less. Half the captains in the fleet would kill to command one of these beauties, but he had been in command for nearly a year but for him it seemed like it was just this morning. Anderson remembered how he became a captain. Back during the dominion war he was 2nd officer on the _scorpion_ a Miranda class light cruiser. It was at chin'toka, those dammed defense platforms hit the ship, and the plasma conduit exploded and killed the captain and XO. He was a lieutenant commander just the second officer many thought Anderson would not know what the young officer was doing, boy where they wrong. After the battle he received a battlefield promotion to captain. At just thirty years old the new captain didn't expect this at least until was forty. But the list of experienced captains was diminishing with every loss so Anderson understood. The crew didn't seem to mind, they thought he was the best choice for the job, but most of them died toward the end of the war.

It was the final battle, starfleet was going straight for Cardassia Prime to end this war once and for all but the dominion wasn't going to take this lying down. They sent a fleet to stop us and that's when it happened. The _scorpion_ was broadsided by a Breen cruiser we took heavy damage, hull breaches on major decks and the core was going to breach. I ordered an evacuation and beamed what was left of my crew to a Romulan vessel and set a course for one of those dominion battleships. Naturally he wasn't going down with the ship so Anderson locked in auto navigation, barely got to an escape pod and left just as the scorpion collided and took the dominion ship with it straight to hell. He was picked up by the _defiant_ and then found out after they got back to DS9 that he was a hero, that battleship was going to tear apart the Klingon battle line. Anderson was given metals and even got an invite by the chancellor himself to visit the home world to be properly congratulated but that did not make up for all the men and women who died on the _scorpion. _

And it was then that captain Anderson was brought back to reality by a call from the bridge.

"_Captain, you better get up here"_

He stood up straightened his uniform and walked through a set of doors and out to the bridge.

"Captain we're receiving a badly garbled distress signal" his first officer, commander Lisa Baker said as she moved to her chair next to the captain. She was a woman in her late twenties with long brown hair which she kept in a bun.

"Source?" Anderson asked as he settled into his chair.

"The 5th planet of this system" she said pointing to the viewscreen where a star map was displayed. "Its not that far off our route to Copernicus station."

"Alright let's take a look. Helm change course to the source of the signal".

--

At warp 9 it took the _Gettysburg_ only 20 minutes to reach the source of the signal. The large cruiser moved toward the planet where their sensors were able to get a clearer picture of the source. On the bridge, captain Anderson stood directly in front of the viewscreen, on it was the planet in question, and the small ship orbiting it.

"Captain the ship appears to have taken damage, we're reading minimal power levels" his ops officer said.

"Lifesigns?"

"Yes, one. Its human, but very faint"

"What kind of ship is it?"

"Unknown" said Baker glancing at her own console "but this appears to be its engineering section jugging from the engines on the back and the radiation levels. The front of the ship appears to have been cut away".

"The Borg have precision cutting beams on their ships" Anderson said "any sign that they're responsible?"

"I'm not detecting a Borg weapon signature on the ship, or any sign of transwarp activity in the region" said Baker "plus its highly unlikely that they would leave a single human alive on the ship".

"Captain, the vessel's orbit is decaying" said the ops officer.

Captain Anderson made up his mind; "alright prepare to beam the lifesign directly to sickbay".

"Captain" said the ops officer again "the transporter can't lock on to him. There is some kind of interference".

"Alright lock the tractor beam on to it and we'll pull it away from the planet. Then beam into an area where there isn't any interference. Anderson ordered Commander, I want you to lead the away team get over there and get that human ready for transport, then download the ships computer records. Lets see what their logs can tell us".

Baker looked up at him, "captain, there is no atmosphere or artificial gravity functioning on the ship. Oh well I guess its time for the suits".

"I'll have commander Collins and a medic meet you in the transporter room" said Anderson as Baker stood up.

"Aye sir" she said as she walked to the turbolift.

The captain said to himself "this is going to be a long day".


	3. Chapter 2: so called rescue

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 2: so called rescue**

"_157 years that's how long it's been, 157 years"_ Cortana thought to herself as she performed her annual systems check. She started this whole hibernation thing about a month after they were stranded. She wrote a program to wake her from stand-by mode, periodically to check on the Chief and the ship. She hoped it would extend her lifespan long enough until they would be rescued, but it looked like the plan was going to fail. The reactor was simply running out of power, there wasn't even enough left to power the sensor array and according to her estimates if she went into hibernation again, in 20 years there won't be enough power to revive her from stand-by, and another 15 after that... the cryo pod would fail. She considered reviving the chief but that was risky with power levels so low and what good would it do them both, but she could at least tell the chief how she feels. "No" Cortana said that was selfish according to her ethics subroutines. Plus they could still be rescued in the next 35 years, but after a century and a half it was likely that the UNSC just considered them dead. With that thought she was about to go into stand-by when the _dawn_ was hit with something.

"What was that" Cortana said to no one in particular.

She risked powering up an external camera to find out what caused the bump hoping it was a UNSC ship but was surprised at what she saw. It was the most unusual kind of ship that anyone saw and it didn't match anything in her database of covenant or UNSC ships. It had an oval shaped front with another section attached underneath, and that part sported two pylons near the back which had what she was guessing were cylinders attached at the top, but they glowed blue. The ship was emitting a blue beam that encompassed the _Dawn_ and was pulling it away from the planet that she discovered they were heading for. But the weirdest thing was the English writing under the saucer, **NCC-61591.** It had to be a human ship and considering the amount of time had past it was certainly possible that earth developed ships like that. So she activated the revival process on the pod. suddenly four people in what she guessed were EVA suits appeared in a flash of blue light. Cortana decided to play it safe and deactivated the holo projector and she just watched them wit the camera.

Commander Baker and her team materialized a few feet away from the human biosign in their EVA suits. She was not fond of them due to a slight case of claustrophobia, but the doctor had given her something for it before they beamed out. She still felt quite uneasy as they explored the derelict ship. She ordered the team to fan out and the chief engineer, lieutenant commander Collins and his assistant walked over to a console and began setting up the data transfer.

"Hey take a look at this" said the medic, leaning over some kind of pod.

Baker walked over and peered into the pod, she did not know what to make of the armored behemoth inside. Her tricorder indicated that the human biosign was coming from within the armor. Her tricorder also indicated from the amount of sub-zero gases in the pod that he was in a state of suspended animation. Which meant that Baker couldn't venture a guess as to how long he'd been in there. Thankfully, her scanner sniffed out some carbon traces in the gases and a few keystrokes later an analysis came back in. The guy had been in there for at least 150 years... possibly longer. She jumped back in surprise as the lid of the pod creaked open, the cryo gases leaked out and produced a fine mist.

"It wasn't me" said the engineer, "the process must be automated, it might have something to do with the fact we're here".

"Alright, slap the transporter enhancer on him and lets beam out" she said feeling her claustrophobia returning. "Commander hurry up and download the computer files" she said to Collins. She tapped her suit's communicator unit and said "baker to Gettysburg the "person" is ready for transport".

_"Stand by we're getting the signal lock… energizing now"_

Cortana could only watch hopelessly as the chief disappeared in the same blue light that brought the strangers in. One of them was interfacing a box shaped device with a computer terminal, she herd them call it an "optronic data core". Cortana saw it as her only way out and to possibly find the chief so she began to compress her program and re-wrote it to disguise her profile so they won't realize she is an AI, and she said to herself

"Here goes nothing". And she uploaded herself to the data core.

"Alright, commander. Download finished" said Chief Collins.

"Good, now we can get out of here. This ship gives me the creeps". She tapped her communicator unit again, "baker to _Gettysburg,_ 5 to beam out".

And with another flash of blue transporter light they were all gone, but they were bring back an unexpected guest.


	4. Chapter 3: unexpected guests

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 3: unexpected guests**

"Doctor, what can you tell me about our guest?" captain Anderson said walking into sickbay and facing the ships temporary CMO. Who also happened to be a hologram, but not just any hologram, but the one from _voyager._ He was a passenger on the _Gettysburg._ They were taking him to the Copernicus research station in the beta quadrant. The ship's normal CMO was called away on family business, so the doctor was more than willing to fill in.

"Well I've been able to determine that he is indeed human but I can't get this suit off him. I've adjusted the tricorder to cut through the interference caused by its power source and aside from some mild skin irritation he appears to be in good shape. But I've found evidence of prior injuries, some of them pretty severe and according to these readings, his anatomy has been significantly altered. Take a look at this".

He showed the captain over to a display on the wall where he brought up the bio readings.

"His bone structure appears to have been reinforced with some kind of metal-ceramic compound. I'd imagine it would be pretty hard to break them. Also, his musculature has been altered with a unidentified protein complex, increasing his overall strength, he could probably lift several times his weight. He also has a neural implant at the base of his skull which interfaces with a shunt in his suit's helmet, along with that his other senses have been improved, like his eyes for instance. The capillary blood flow in his eyes has been improved. This could effectively give him literal night vision".

"Impressive" said the captain.

"I believe these enhancements are artificial and it looks like he wasn't born with them, according to my scans he was most likely augmented during adolescence".

"Did _voyager_ ever encounter something like this when you were in the delta quadrant?" Anderson asked.

"Nothing on this scale" the hologram replied "this sounds a lot similar to the augments of the mid 21st century. During the eugenics wars."

"Can you wake him?"

"If I could get his armor off, but with all the augmentations I have no way of knowing how his chemistry would react to a stimulant. Its possible he just suffering the after effects of his cryo sleep, he might wake up on his own".

"Alright, I'll have Chief Collins come up and see if he can open him up, let me know what else you find". And with that he left sickbay, heading for engineering to see what the ship's logs to tell them about their big green friend.

--

Cortana couldn't tell how long she was in the data core but it came as a relief as she detected an upload in progress. So she sneaked into the transfer and embedded herself in the computer. The AI uncompressed her program and began to get her bearings. There was so much information at her fingertips but decided to play it safe, not knowing what security measures were in place and she focused on the historical records, trying to find out what happened. But their history was radically different, and even the date was off it should be 2709 but their chronometer says the year is 2377. It had to be a fabrication but why would they put it here unless, and a wave of panic came through her system. _"They must know I'm here, they're trying to lure me into a trap by trying to find out more about the discrepancies". _Even though she didn't detect any taps in her system she quickly began searching for any sign of the chief.

* * *

"Ah, and here we are" said the tenth doctor as he began powering down the TARDIS.

"So where are we this time?" asked the doctor's most recent companion, Donna Noble. "A space station, some far off planet?"".

"Nope, feudal Japan. That's about 500 years into your past".

"That's it, just 500 years. I expected something like a thousand years".

"Ah, but there is some very fascinating creatures at this point in time".

"Really, I doubt that" replied a skeptical Donna. "The most we're going to find is some ninjas doing some... ninja stuff."

The doctor began to move toward the door then began to open it. "Well have a look outside for yourself" he said.

And as if on cue, as soon as the doctor opened the door 4 people crashed through the doorway and into the TARDIS.

"_The doctor wasn't kidding, these people were strange"_ Donna thought to herself.

One of them, a female was carrying a giant boomerang in one hand and a strange cat in the other. Two of them were guys but one of them had long silver hair and she couldn't believe her eyes, dog ears. The last one was a girl, she was clutching some kind of animal and the clothes she was wearing were kind of familiar.

"What the hell just happened!" screamed the silver haired boy "this is probably another one of naraku's tricks!".

"Inuyasha, get down" one of the girls said as she ran up and pushed him to the ground just as a purple energy beam entered through the open doors and struck the center console on the TARDIS, which sent out a shower of sparks.

"Doctor!" Donna screamed as the doctor made his way to the console he had a grim look in his face. Then the TARDIS doors slammed shut. The doctor reached the panel and said, "oh no".

The TARDIS began to shake violently and the lights began to dim. The doctor looked at them all and told them to hang on as the TARDIS spun violently out of control.


	5. Chapter 4: introductions and revivals

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 4: introductions and revivals **

Cortana franticly searched for any sign of the Chief, careful to make sure she didn't set off anymore security measures. Cortana was able to tap into the ship's visual sensors and then she found him. The Master Chief was lying on a bed and from what she could tell, he was just unconscious. So she tapped into the ship's internal communications and contacted his suit. Cortana could only do this for a few moments before being detected so she had to make this quick.

"Chief… can you here me, chief?" she said, hoping she would respond. Cortana could feel her time running out. "Chief, please" she cried, "Please, John!".

--

"Cortana" the chief said, he thought he herd her voice just then. The chief slowly began to get up feeling groggy and his skin was killing him. One of the after effects of cryo sleep if you go in wearing something over your skin. He looked around and saw a bald man standing in one corner, he looked over as saw the spartan getting up. He said "ah you're awake", and he walked over and stood next to the Chief.

"Try and relax, you're safe here. I'm a Doctor, you have no reason to be afraid", he then taped the pin on his chest, "Doctor to Captain Anderson, our guest is awake".

--

The captain strolled into engineering to see what commander Collins has gotten from the computer files. He was standing at the console in front of the warp core, padd in hand

"Report, chief"

"Well captain, I'm afraid I can't tell you much. All the data we downloaded appears to be encrypted. But the strangest thing is from what I can tell, the data was encrypted after we downloaded it. I'm running a diagnostic now to see what happened".

Just then the captain's communicator chirped and the doctor's voice came through,

"_Doctor to Captain Anderson, our guest is awake_".

"Understood doc, I'm on my way". He turned to leave for the turbo shaft. "Chief, keep on it" the captain said as he was leaving.

"Understood". The Chief was about to go back to his decrypting work when another engineer called him over to his station, "Ok what do ya got?" he asked.

"Chief, I was a routine check on the computer core when I found this".

Collins looked at the screen for a moment before seeing what that ensign was pointing out.

--

The captain strolled into sickbay to see the green suited guy sitting on the biobed with the doctor standing next to him "Ah I see your awake, I'm captain Marc Anderson, commanding officer of the federation starship USS Gettysburg, and you are?".

All of a sudden the man stood at attention snapping of a crisp salute, he must have been at least 7 feet tall.

"Sir, Master Chief petty officer, Spartan-117"

"At ease, Master Chief" the captain replied kind of awkwardly.

He then moved to a more relaxed posture, "captain, could I ask you what year it is?".

"Of course, its 2377".

"That's impossible!" the chief responded.

The captain had a puzzled look. "ok how do you figure that?" he asked the Spartan.

"Because when I went into cryo stasis, the year was 2552"

That almost made the captain's jaw drop but then he came up with a startling thought. "Doctor, I want you to run a quantum resonance scan on the chief here".

The doctor at first seemed puzzled, but then understood. He took out his tricorder and scanned the chief.

"What's going on?" asked the chief.

"Just testing a hunch" replied the captain, "well doctor"

"It would seem your hunch is correct. the Chief here has a different quantum resonance signature".

"Ok could someone please tell me what's going on?" asked the chief.

"All right bear with me Chief, all matter resonates on a quantum level which has the same signature, but you don't have the same signature as me or any other matter on this ship. To put it simple Chief, you're from a parallel universe".

Now that the chief understood from his may classes on quantum physics when he was younger. But it gave him a sinking feeling, what if they didn't have a way to send him back? But just as he was about to ask that question an alarm klaxon sounded and sickbay was bathed in a flashing red light. The communication device on the captain's chest chirped and a voice came through.

_"Collins to Anderson, captain, we have a problem"_

"Go ahead, commander, what is it?"

_"Captain, the main computer appears to be infected with some kind of virus"_

"Show me". And with that the main monitor in sickbay switched to a diagram of the computer files, and the virus was highlighted. What ever it was it was complex.

_"We isolated it in the sickbay system"_

That sent a chill down the captain's spine, "Doctor you better transfer your program to the mobile emitter".

"Agreed" said the hologram and he went into his office. The captain then turned to face the display, it was then the Master Chief recognized those lines of code.

"Alright, prepare to purge the virus" the captain ordered.

The chief barked out, "wait!"

The captain turned to face him, "and why should I do that?".

And it was then that he got his answer, the holoprojectors came to life and a figure of a woman appeared. But she was very strange, her skin was blue in color and her whole body appeared to be comprised of lines of code. She looked like someone in their twenties and apparently the chief seemed to recognize her.

"Cortana"

"Chief" the hologram said,

"_Cortana must be its name"_ the captain said to himself. "Will someone explain what's going on?" asked Anderson.

The chief responded, "sir, I should have told you about Cortana. She is an AI construct, she's harmless and I assure you she is no threat".

"All right, Chief, for now I'll believe you, but I must ask that Cortana here be moved out of the ship's computer".

"That's not a problem, my armor is designed to carry Cortana"

"Ok we'll get this sorted out, then I want you to meet with me and my senior staff" said Anderson as he left sickbay.

Cortana walked over to john and said "watch this". She put a hand on his arm and it didn't pass through.

"Solid?" the chief asked.

"Apparently their tech is way beyond the UNSC and even the covenant" she said "the holographic projectors are just the start".

The chief didn't care; he was just relieved she was ok.

* * *

She awoke with a shock gasping for breath panicking not knowing where she was or what was happening. She herd voiced telling her to calm down then she felt something press against her neck, she began to feel groggy and with that a sedated commander Miranda Keyes fell back on the bed.

* * *

The doctor was struggling to keep control of the TARDIS as it spun violently out of control to god knows where. Donna and their 4 guests were at the other end of the room when the TARDIS finally stopped but then all the lights went out.

"Oh not again" said the doctor trying to get the controls to work but no luck. The doctor walked over to see if everyone was alright but was met by the silver haired boy's sword.

"All right I want to know what the hell is going on!" he said,m pointing the sword at the doctor's chest. Then the same girl who was wearing a modern Japanese school girl's uniform said

"Inuyasha, sit".

The beads around his neck glowed and pulled him to the ground. The girl apologized for Inuyasha's behavior and gave her name as Kagome and she introduced her other friends. The demon slayer Sango and her pet demon cat Kirara, the monk Miroku, and the fox demon Shippo. Then there was Inuyasha who was half demon and half human. Donna was surprised to here that Kagome was from the same year as herself. The Doctor introduced himself, then explained that the TARDIS had to have been transported to a parallel universe and the TARDIS doesn't function in parallel universes.

"So I say we have a look outside", and with that the doctor donned his coat and opened the door.

The six of them walked out onto a grassy plane and looked around, of course after the shock of the size of the TARDIS on the outside. Inuyasha said he smelled other humans nearby and so the group set out in the direction of the scent.

* * *

Commander Keyes woke up in a hospital bed with lord hood at her side.

"Welcome back, commander"

"Admiral, how long was I out?"

"Commander, the question you should be asking is how long you were dead, its October 15 2554".

It made her freeze when he said those words, dead; the last thing she remembered was Johnson asking her to kill him.

"Commander, it was damn luck that Johnson got you to the cryo on the _aegis fate_ other wise we wouldn't have been able to bring you back". He began to explain that her body was actually flash cloned, they had made tremendous medical advancements while she was dead and her old body had been too badly damaged to anything. But they were able to transfer her mind into the new body; she was also the first person to undergo this procedure. But all this didn't matter, she was shocked that she was alive but then she found out about what happened on the ark, the death of truth and Johnson, then the Chief and Cortana.

"Commander, I wish your revival was under better circumstances, let me fill you in on what's happened. The remaining covenant races weren't ready to give up so easily but thanks to the help of the elites we're on equal footing, and we've been joined by the remaining hunters and grunts. The covenant loyalists however have a new prophet who calls himself retribution. They managed to sneak a fairly large battle group past our lines on a direct course for earth; they also managed to get their hands on one of our NOVA bombs.


	6. Chapter 5: universes collide

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 5: universes collide **

Spartan III Ash-G099 was walking around, still in his SPI armor, thinking about what was left of team saber, just Mark, Olivia and himself. He felt like he lost his favorite siblings when Holly and Dante died. He missed them both, especially Holly, but he could only guess how the other Spartans were feeling. They had lost two of their teammates as well. Linda had taken Will's death pretty hard; she was going out of her way to avoid everyone, even the el-tee. The doc still had no way out of this bomb shelter they've called home for the past week or how to get team katana out of the slipspace field pods.

--

Linda was sitting on a hillside a few clicks from the camp looking out over a grassy plane. Her armor helmet was off and she was thinking about Will. Linda has secretly loved will but she could never muster the guts to tell him, now he was gone forever. She was barely able to hold back the tears. And it was then she noticed movement out in the distance, she put her helmet back on, grabbed her sniper rifle and used its oracle scope to get a better look. Linda saw what appeared to be six people walking around, they were human, also strangely dressed and the lead one was sniffing the ground. Linda then activated her TEAMCOM to inform the el-tee.

--

Fred looked over what he designated alpha base and at his new blue team, the remaining Spartan-IIs, himself Kelly and Linda who was doing recon. There were also the Spartan-IIIs, the 3 kids from team saber plus Tom and Lucy all of them encased in their SPI armor. The only non Spartans with them were Dr. Halsey, creator of the Spartan-II and chief petty officer Mendez, Fred's old drill instructor.

Suddenly Fred's comm flared to life with Linda voice, _"Fred I've got 6 contacts… they all appear to be human". _

"What, but we're the only ones here" he said almost in disbelief, "alright where are they heading?", he got silence. "Linda?".

"_El-tee they're heading for me… I'm running for the tree line"_.

Fred turned to his team, "Blue team we have a situation, Linda's in trouble. Kelly get out there now. Tom and Lucy stay here and guard the doc and Mendez. Everyone else gear up we're going in".

--

Linda was watching them through her scope as one of the girls hopped onto the silver boy's back and some large cat appeared out of a fireball, and two more got on its back then it started to fly. Leaving the last two, a guy in a trench coat and woman to run on foot, but they were all heading for her.

She said into her comm, "el-tee their heading for me… I'm running for the tree line". Then made a beeline for the trees. They most likely saw her but the thick foliage might keep her safe from that flying cat, for all she knew it breathed fire. She picked up two contacts on her motion tracker at her six so she darted behind a tree and waited a few moments. But when she came around the guy with the trench coat and his friend were standing right in front of her.

"Oh hello, I'm the doctor and this is Donna" pointing to his friend

* * *

Anderson couldn't believe the chief's tale, he was in the observation lounge with most of his senior staff listing to the chief tell them about his universe. The UNSC, the covenant, the flood and the forerunners. Finally how they ended up stranded in this universe for the past 160 years.

"Alright Collins" the captain said to his engineer, "any idea how we get the chief home?".

"Well sir we were able to find the aperture of the anomaly that brought him hear and with a few modifications to the deflector array we could open it up again. It should lead to its terminating point this would take a couple of hours. But the chief's ship is too badly damaged and a shuttle won't survive the trip so the only option is to take the Gettysburg through".

Captain Anderson thought it over before addressing the crew "Alright it's settled then. We'll go through as soon as the modifications are done. In the mean time we'll drop a buoy for Starfleet with all our logs in case we don't make it back, dismissed".

With that everyone left the room then the master chief walked up to him to ask if he could get a few things from the dawn. Not knowing what they would face when the _Gettysburg_ reached the other side, it couldn't hurt to be prepared so he granted the Spartan's request, then went to his ready room to write the message for Starfleet.

The chief got into a turbolift and went down to the transporter room.

"So what do you think of them?" Cortana asked him on the way.

Personally I'd wished we'd met them sooner" the Spartan replied. "They could have helped us in the war, maybe Reach and the other Spartans would still be here".

"Well from what I learned from their computer is that they don't like to interfere with the affairs of other races" said Cortana. "But look on the bright side, at least the war is over… as far as we know".

"Too many good people had to die, Cortana"

* * *

Lt. Colonel Cameron Mitchell knew something was wrong the moment they entered the supergate. When their ship, the _odyssey_ emerged they should have been in the Ori galaxy, but there was no supergate on the other side, no black hole and no Ori ships. And that IOA agent Merrick wasn't making him feel any better. He turned to look at Lt. col. Carter, manning the station next to him.

Any idea what happened to the gate? he asked

"I've just finished another scan" said Carter "I can't detect a supergate or anything within 4 million kilometers of the ship".

"Sam, I think we have to risk activating the Asgard core".

"Cameron, that'll alert every Ori ship to our presence" replied Carter.

"Sam, look around. There are no Ori ships and the Asgard sensors might be able to tell us why… but just in case activate the cloak".

"Ok, cloak's on and I'm powering up the core... now". She waited a few tense minutes before she spoke again, "ok Cam, I've completed the scan there are no Ori ships anywhere in this system but there are some strange energy readings coming within this system".

"Alright seems as good a place to start as any. Major Marks" Mitchell said to the officer on his left, "set course for that energy reading"

* * *

The Master Chief pitched the nose of the pelican dropship up as he glided out of the _dawn's_ hangar bay. The remains of the frigate were being sent on a ballistic trajectory by the _Gettysburg_, and would burn up. The Spartan had already salvaged what he could from the ship, including the pelican he was using.

"So what exactly did you learn from their computers?" The Chief asked Cortana.

"A little about their tech, not enough for us to replicate when we get back to Earth."

"What about their people? I saw some strange looking aliens wearing their uniforms."

"From what I read, Earth was a founding member of something called the 'united federation of planets'. Its about 200 years old, local time, and it comprises over 150 planets with Earth as their capitol."

"What about the _Gettysburg_?" the Chief asked.

"Its part of starfleet, the federation's military and exploration branch" Cortana explained "the _Gettysburg_ is one of their heavy cruisers along with the fleet's flagship, I believe the name was _Enterprise." _

"Anything on their weapons?"

"That information was restricted, and I doubt I'm going to get another look inside their computer any time soon."

The Spartan turned his attention to the controls as the dropship approached the back of the Gettysburg. The bridge gave him instructions to land in the main shuttlebay, located at the back of the saucer section. The center door slid down and the Chief glided into the shuttlebay. He was surprised to find crewmembers walking around the bay, without any protection on, but Cortana told him they had mastered forcefield technology. The Spartan set the pelican down and moved into the troop compartment which was loaded down with crates of supplies. He moved out of the ship and squeezed past the warthog he had tucked underneath.

"Planning on doing some hunting?" Collins asked as he came over, scanning the pelican.

"Probably" said the Chief as he unloaded one of the crates and inspected the twin jackhammers inside. He then moved on to a crate of MA5C assault rifles. Collins started scanning all of them.

"These are projectile weapons!" he said in amazement.

"Don't you use them?"

"No, our hand weapons are all energy based and unlike yours, they come with a sun setting" said Collins as he scanned the warthog. "this thing uses an internal combustion engine. I thought you were from the 26th century in your universe."

"We are" said Cortana "the fuel we use is a synthesized carbon compound that emits zero pollutants, its more efficient to use an combustion based form of power. The pelicans operate on a similar system. However, our starships are powered by fusion based engines.

"I'm sure some of our scientists would kill to get a chance to check out your universe" said Collins as he entered the pelican. His tricorder started beeping and the engineer found the source, a small half-sphere shaped device sitting on one of the crates.

"I was going to tell you about that" the Chief said as he noticed him scanning.

"My tricorder says this thing could put off a thirty megaton blast!" said Collins "you need the captain's permission to keep this aboard."

"Trust me, if we run into my 'old friends' on the other side. Then we're going to need the extra firepower. You don't know the covenant like I do."

* * *

Miranda Keyes along with lord hood strolled onto the bridge of the repaired MAC station Cairo, they had just gotten word that the covenant fleet had entered earth's solar system, one of those ships was carrying a NOVA bomb. She was surprised to find The Arbiter standing in front of the main display, looking at the fleet deployments. They had 43 ships, 15 were elite ships and only two were those new hybrid ships, all they could assemble on short notice. The covenant had 69 ships which was more than enough to cut through and use the NOVA on Earth.

"Admiral, commander, it would seem that this war is at an end" The Arbiter said as they walked up to join him.

Lord Hood replied, "Don't count us out yet, we still have 22 MAC stations. That should even the odds".

"Were it so easy" said the arbiter, "the fleets will make contact in 2 minutes".

"Sir, do we really stand a chance?" asked Keyes.

The admiral gave the grim reply, "no, not against a NOVA bomb. But we'll give those bastards hell and we'll go out fighting".

The arbiter turned to face them, "our fleet is in range to fire" he said.

"Admiral, we've got a new contact. Unknown classification" said an officer manning a station behind them.

Hood turned to him. "is it a forerunner ship?" he asked, this situation was eerily familiar.

"Negative sir. Wait, its hailing us on UNSC E-band".

What happened next made all three of them freeze where they stood.

"_This is Spartan 117, does anyone read me"._

* * *

Linda instinctively brought her sniper rifle to bare, it was out of ammo but she hoped they wouldn't notice.

"Whoa, we don't want to hurt you" said the Doctor as he threw his hands up along with Donna, "We're just looking for a way home".

"Like I'd believe that… this is some forerunner trick" spat Linda.

"That's what you think!" came a voice from behind".

Linda turned her head to see the silver haired boy pointing a very large sword at her. "What kind of demon are you supposed to be?"

"The kind that's going to kick your ass" said a voice from behind him as Kelly's foot made contact with Inuyasha's chest sending him hurtling backwards and causing him to drop his sword.

"So there are two of you this will be fun" was his smug reply.

"That's not going to happen, dog boy" said Kelly.

Linda still had her rifle trained on the other two but then a crashing noise came straight for them as trees were being knocked down by what Linda could tell was a giant boomerang. She ducked but a falling tree pined her to the ground. Kelly was still fighting the dog boy when some kind of force began to pull Kelly away. Linda saw what it was; the other strangely dressed guy had a hole in his hand that was pulling everything into it, including Kelly.

"No!" Linda cried as Kelly was being sucked in. She was still pinned by the tree forced to watch helplessly. But then all of a sudden, black hole guy covered up his hand as he screamed in pain, Linda saw a bullet wound on his arm. It had to be Fred and sure enough she heard his voice.

"Alright all of you on the ground now or you'll end up a lot worse than your friend with the vacuum hand!".

That was when Donna decided to speak up, "hang on we've done nothing, our ship's broke down that's all now will you quit pointing guns around spaceman".

"Not likely Donna", Inuyasha replied "all these demons understand is fighting and I would be glad to show them".

"Just you try kid", said Fred.

Then an arrow, surrounded in a purple energy field, screeched past Fred's head and hit a tree, which exploded.

"Alright drop the weapons", said Kagome but before she could react, team saber appeared and surrounded her, the doctor then broke the silence.

"Look I think this is getting us nowhere. Now I suggest we just try and talk this out".

"Fine we'll talk, but I must ask for your weapons, consider it as a good faith deposit" replied Fred.

* * *

Lord Hood couldn't believe what he was hearing; it sounded like the Master Chief, but was it him? "Master Chief, that had better be you?", said hood

"_Sir, I assure you it's me and as you can see I've brought some friends to help… sir, the sensors here are detecting a radiological signature aboard one of the covenant ships"_

"Chief, listen to me carefully. That's a NOVA bomb, you've got to take out that ship" said hood.

"_Understood sir, we're on it"_

--

And with that the channel was closed, Captain Anderson returned to his chair on the bridge, the Chief was standing next to him.

"Give me a tactical analysis" Anderson ordered.

"Our sensors indicate the alien ships are driven by some kind of plasma based reactors. I'm picking up traces of deuterium and tritium. Their shields are also inferior to ours according to the scans of their generators."

"_Inferior"_ the Chief thought to himself._ "They really were more advanced than the covenant. A bunch of humans no less."_

"Helm, plot a course to take us by one of those stations and prepare to beam the Master Chief over" Anderson ordered.

"Captain, I thought you were going to engage the covenant?" The Chief asked.

"Chief, starfleet forbids me from interfering in the affairs of other cultures, we call it the prime directive. Firing on those ships would be a violation of that" Anderson explained.

"Captain, there are billions of people on Earth!" Cortana pleaded from inside the Chief's MJOLNIR armor "you can't be that heartless".

"Cortana, if it we're up to me I wouldn't hesitate to fire, but I swore an oath to the federation and that includes upholding the prime directive. You of all people should know what that's like."

The Chief knew that Anderson was right, his hope that the federation could actually save the UNSC was slowly slipping away.

"Captain, the alien ships have released some kind of plasma charges... targeted at us! Time to impact: 45 seconds" his ops officer reported.

"Red alert!" the captain cried, "raise shields!"

The lights on the bridge dimmed and flashing red illumination came on, several of the displays changed to their default red alert format. The Chief moved to the back of the bridge and grabbed one of the handholds near the master systems display. Expecting a rough impact. But the ship was only slightly jostled b y the plasma impact. The Chief returned to the captain's side.

"All hands to battle stations, charge phasers and load torpedo bays" Anderson said to his tactical officer, Lieutenant Cheney. Who also happened to be a descendant of an American vice-president, involved in a hunting accident. Scan the covenant fleet and find the ship carrying the NOVA bomb.

"I don't get it, why are you fighting now?" The Chief asked.

"The _Gettysburg_ being fired upon is an act of aggression against starfleet" commander Baker explained "it gives the captain just cause to violate the prime directive".

"I've got the ship" said Cheney "sending coordinates to the helm."

"Fire phasers as soon as we're in range" Anderson ordered.

--

Lord Hood watched in amazement as the twin plasma bolts washed over the shields of the new ship. It turned and charged straight for the covenant fleet. A crimson orange beam emitted from the front of the ship and struck a covenant carrier. Their shields held for only a few seconds before collapsing, and the beam cut into the hull boiling away the armor and slicing clean through the carrier. This was followed by three more beams, then two red balls of light left the ship from a bump on the underside of the saucer and made contact with the carrier, obliterating it in a manner of seconds. After the carrier was destroyed the covenant ships turned and accelerated into slipspace, hood couldn't believe what he just saw.

"Did we just win?" Keyes asked.

"I truly don't know commander". An ecstatic hood replied

--

The Chief felt good being aboard a UNSC station again; Captain Anderson accompanied him to the Cairo for the debriefing and to be congratulated by lord hood. The chief was also shocked to find Miranda Keyes there as well. Hood explained the procedure that they used to resuscitate her. The arbiter was there as well and apparently he became the leader of the covenant separatists.

"Captain Anderson" said lord hood as he shook the captain's hand "the UNSC owes you a debt of gratitude for what you did out there".

"It wasn't much trouble" Anderson replied.

"So, Master Chief, care to tell me just exactly where you've been and where you found that ship?" Hood asked.

He took the group to a conference room where the Spartan explained what he and Cortana had learned in the parallel universe. When he was finished, the Chief then asked where the rest of blue team was. Lord hood gave him the news.

"Chief, I'm sorry but they were killed in action 2 years ago".

Then that was it he really was the last Spartan. "may I ask how sir?"

"Sure" he motioned the chief over to a monitor and accessed a video file. "this was taken from a prowler over a planet called onyx. They were sent there to retrieve some forerunner tech that was reported to be there. Unfortunately the planet broke apart, but it took out a Covenant fleet in the process".

"Wait, Chief" Cortana said from inside his suit.

"What is it?"

"You're not going to believe this, but they may not be dead".


	7. Chapter 6: encounter at onyx

**Just in time for Independence Day, happy 4th everyone **

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 6: encounter at onyx **

"Ok could we go over this again?" the Chief asked Cortana They were in the briefing room on the Cairo along with hood, Anderson, Keyes and The Arbiter. Cortana was explaining about some forerunner plan.

"All right I'll go over it again" said Cortana from the holoprojector in the middle of the table. "The forerunners placed their own version of bomb shelters in this galaxy. They were designed to ride out the halo detonations, its possible they got into it before the planet exploded".

"How do you know this, Cortana?" asked hood.

I had the information in my system from the files I absorbed at the first Halo Cortana explained I only started looking them over on the _dawn_.

"How do we know that this bomb shelter survived the planet's break up?" asked Anderson

"We don't" replied Cortana "but this is the forerunners we're talking about. If this shelter could survive a halo detonation it could withstand the planet exploding".

"Admiral Sir, we have to go to onyx to see if they survived" said the chief

Hood replied, "Chief, I'd like nothing more but I can't risk sending a ship on what I know is a one way trip. We all saw the visual logs, those sentinels will cut you to pieces before you get close. I'm sorry son request denied "

"Admiral if I may" said Anderson "we could use my ship, we may be able to mimic a forerunner energy signature using the Gettysburg warp engines. We could approach and use our transporters to beam into the bomb shelter and get the Spartans out if they are there".

"Captain, I don't want you to risk your ship and crew on some wild hunch, plus you have your own universe to get back to".

Anderson had been wondering how to approach what he had just learned "admiral, my engineer tried unsuccessfully to open the portal up again. Apparently it was a one way trip for us. But from what I understand these forerunners were the most advanced race that ever lived and it was forerunner tech that brought the chief to my universe so forerunner tech may be the key to getting my ship home, and there might be a clue at this bomb shelter. Danger or not, it's a risk me and my crew are willing to take".

"Admiral, I'd like to volunteer to go on the mission" said Keyes.

"I will join your quest as well" said the arbiter.

"I'd like to go with the chief too" said Cortana.

Hood was practically outnumbered, "all right I'll approve the mission, Chief. But I can't spare any ships to go with the Gettysburg, if things get hot then you'll be on your own".

"I understand the risk, sir"

"Very well chief, good luck".

* * *

Tarinus, the brute chieftain and brother to the late Tartarus walked into the prophets chambers after being summoned. He entered and bent down on one knee. "noble prophet" he said.

The prophet of retribution turned to face him "rise chieftain".

He stood up "to what do you summon me, holy one?".

"We need to discuss what happened at the home world of the humans".

"Noble prophet, the humans had some kind of new ship. It rained destruction on our command ship carrying the human weapon with strange and powerful weaponry. We were unprepared for this and the fleet master…".

Retribution cut him off in mid sentence "I am not interested in who is to blame, the fleet master did the right thing by retreating and bringing information to me so we may decide the next move. Come here." He motioned the chieftain to stand next to him and they both looked at the display. "This is a system whose coordinates are known only to the prophets".

"Holy one, what is in this system?".

"The repository of the reclaimers, we must gather a fleet and travel to this system and seek out the reclaimers. Only with their council can we overcome this new threat".

"As you wish" and with that he left the prophet's chamber.

* * *

Inuyasha sat with his three other friends and Donna on a grassy hill at alpha base. The doctor was talking to the one they called Fred. They had treated Miroku's wounds but one of them kept what Kagome had called a gun trained at him at all times. They had also taken his Tetsusaiga along with everyone else's weapons, he still had his claws and hoped it was enough to take them. But Kagome had warned him that those gun things could kill him if he got hit in the head. Plus, what would happen to the sacred jewel, they had risked their lives to steal it from Naraku and now they finally had the nearly complete jewel. All it needed was the shard held in a bottle around Kagome's neck. They decided to hold off on informing everyone else of the jewel. He turned to face Donna and said "I hope that doctor is a fancy enough talker like he claims to be".

"Relax Inuyasha" she replied "the doctor knows what he's doing. I think he's been in this situation before so we have nothing to worry about".

Inuyasha looked around at the other strange people. He saw two older people not wearing the weird 'space suits' Donna had called them. They were standing next to 5 strange looking pods, there were two more people wearing the strange suits that made them invisible. Inuyasha herd them call it 'SPI armor'. "Whatever that meant" he said to himself, then the doctor walked over with Fred.

"Well I've talked with the lieutenant here, and he's decided to allow us to stay here if we wanted. Since, apparently there is no way out of this Dyson sphere".

"What the hell is a Dyson sphere?" asked Inuyasha

The doctor then began to explain what a Dyson sphere was and during this that the one he fought with earlier called Kelly gave them all back their weapons.

"So you've been trapped here?" Kagome asked.

"Yes unfortunately" replied Fred "and from what the doctor here tells me your ship doesn't work in this universe".

Then his comm came to life, once again with Linda voice _"Fred you better get over here. I found some kind of tower"._

* * *

Commander Keyes was standing in the officer's club of the Gettysburg looking out of the window. But the only thing she could see was the front of the elite flagship _shadow of intent_. The_ Gettysburg_ had docked in the space between the hangar and the front bulbous section in order to use the ship as a carrier in slipspace because it would take the Gettysburg a full two weeks at high warp to reach onyx. Traveling by slipspace, they would be there in 2 days. She was holding a coffee in her hand she got it out of those wondrous replicators. She had been pondering her second chance at life, _"am I just supposed to go on like nothing happened she thought to herself". _She overheard Captain Anderson talking about letting Cortana back into the computer. The AI said it was so she could use the holodeck to try and cheer up the chief, he granted her request. _"The chief could definitely use some cheering up"_ she thought to herself, and she returned to her coffee and began to stare out the window again.

--

The chief walked up to the big set of doors that read holodeck 3, Cortana asked him to meet him there so he walked into the holodeck and what he saw startled him. It was a nighttime setting but it was the setting, Reach! He was on Reach. The Spartan herd some of the Starfleet crew talk about them but this was amazing. It looked just like his childhood home, even the star pattern was the way he remembered it.

"I'd thought you like it" said a life-sized Cortana from behind him.

"Cortana..." the Chief was speechless "thank you, Cortana".

They sat there on the grassy plan staring up at the sky. The chief had his helmet off for the first time in days.

"Chief, what was it like when you were living here?"

"Most of the time it was painful training, but I liked the times when we went on survival training and we came out to places like this. Those were the best times, it was nice and peaceful."

It was then that Cortana placed her holographic hand on his shoulder "Chief, what will you do… if you don't find them?"

The Chief turned his head and looked into her eyes "I won't stop fighting until they're avenged".

They both sat there for the remainder of the night looking up at the artificial sky.

* * *

Fred along with blue and saber teams, doctor Halsey and the doctor's group approached what they were guessing was a door. Fred looked up the tower which kind of looked like the space needle, only with forerunner architecture.

"Doctor" he said looking at Halsey "any way in?"

She was standing in front of a panel with her laptop open "if I could figure out how to translate these controls I think I could open it".

"Let me have a crack at it" said the Doctor as he came up to the panel, he pulled out a small metal rod with a blue light at the front. Donna said it was his 'sonic screwdriver'. He pointed it at the door controls, hit a switch on the device and they came to life. Then the doors began to move apart.

"Good work" Fred said as the group walked inside. It was dark so they flipped on their suit lights, that's when they saw a translocation platform at the other end. Fred turned to Halsey "Doctor, do your thing".

She began typing away on her keyboard bringing up the program to run the platform.

"Everyone on the platform" Fred ordered.

They all complied and moved to the platform then Halsey activated it, within a few seconds they were surrounded by the yellow rings of light, then it was over. But Fred and most of the others felt like their insides had been twisted around. They ended up in some kind of control room and it was covered in forerunner holographic controls. Halsey and the doctor walked over to the biggest control panel in the room, Fred then joined them after a few minutes.

"Report, doctors"

"Well I've been able to translate some of these words this is apparently the master control panel for some kind of field, it may be the field that's keeping the portal shut" said Halsey.

"Can you shut it off?"

"I think so"

"Then do it"

Then they returned to looking at the panel. The Doctor pointed to a yellow button and said "this has to be it".

"Try it" said Halsey"

And he pushed it down, nothing happened, nothing that they could tell.

* * *

It was a tense moment on the bridge. Anderson was sitting in his command chair with baker in her chair to his right and commander Keyes to the one on his left with the arbiter and the chief standing behind him. The _shadow of intent_ had dropped them off at the Oort cloud and would hold position until they returned and with that the _Gettysburg_ went in under her own power. Collins had just finished the modifications to put out a forerunner energy signature when they approached where onyx used to be only to find a large debris field, surrounded by trillions of sentinels.

"By the rings!" the arbiter said

"Ops, report" said the captain.

"No sign that they are preparing to attack, sir. It looks like we pulled it off".

"All right then, move us in and lets see if we can find this bomb shelter".

The Gettysburg glided past the rock and sentinels when its shields hit a ripple in space. Before they could backtrack, the ship had entered a compressed slipspace field.

"Report?" Anderson demanded.

"Sir, look" said Baker as she pointed out the viewscreen. It was pitch black, due to the lack of stars in slipspace. But they didn't need them in order to see the large sphere the _Gettysburg_ hung over.

"Captain" said the science officer "according to the energy readings I'm getting, there's a G-type star in the center of the sphere. Which means its a Dyson sphere. Not only that, its also encased in a time dilation field.

"Can you tell in which direction time is flowing?" Anderson asked

"Yes, it appears time in the field is slowing down. For them it may have felt like only a few days have passed".

"Can we beam in?" asked Keyes.

"Not through a time dilation field, commander" Anderson explained "we need a real-time location to beam you into. Otherwise, you'd be atomized as the matter stream passed through the field"

"Wait sir, the field just disappeared" reported the science officer, "and I'm picking up human lifesigns".

"Cause?"

"Unknown, captain"

"Well commanders, the mission is still on. Prepare to beam out".

* * *

Shippo was sitting on the hillside at alpha base with Kirara "humph, why am I always left behind? That smug Inuyasha, this was probably his idea".

Tom and Lucy were once again on guard duty, Tom didn't like being left behind all that much but orders were orders.

"_Tom, Lucy, I've got contacts, unknown number. I can't tell what they are they're too far out for my field glasses"_ said Mendez over the radio _"they're heading for the tower"._

"Understood, Chief. Get back here" he then got on TEAMCOM to inform the el-tee.

--

Fred and the others were waiting in the control room when Tom gave him the news.

"Alright Linda, Kelly and Inuyasha you're with me. Everyone else, stay here and protect the docs"

The four of them made their way outside where Inuyasha caught their scent and started heading off, they followed.

* * *

On board the_ odyssey_, colonel Mitchell had just returned to the bridge along with the rest of his team, Dr Daniel Jackson and Teal'c. Carter had in formed him that they arrived at the source of the energy readings.

"Sam, what do we got?" asked Mitchell

"There are a lot and I mean A LOT of those little things flying around" said Carter. She looked at her screen again "hang on, I'm picking up another ship".

She hit a few keys on her console and brought up an enhanced image on the main display to their left, they were stunned by what they saw. Daniel then spoke up.

"Hey guys, doesn't that look an awful like…"

"The _Enterprise_" Mitchell said, finishing his sentence. The ship looked just like the one from the most recent movies. "Carter, how the hell is this happening?".

"I haven't got a clue but according to the sensors, that's an honest to god _Enterprise_… whoa hang on a sec" carter said as they watched the _Enterprise_ seem to disappear through a ripple in space.

"Sam, what just happened?"

"I don't know. Asgard sensors can't penetrate the energy field"

"first the supergate disappears, then the _Enterprise_ shows up" Daniel remarked "the Ori galaxy is an unusual place"

"Cam, I'm picking up a massive distortion in space" said Carter "its coming from right behind us".

* * *

The Chief and his team materialized a short distance away from a large tower. They were following commander baker who had detected a large batch of lifesigns on her tricorder, coming from the tower. She then reported 4 of them were heading straight for their group so the Chief went ahead. The spartan picked up the contacts on his HUD, so he keyed his COM and whistled the Spartan's all clear code.

Oly Oly Oxen Free

He got the countersign on his TEAMCOM channel, the one reserved for blue team. _"All out in the free, we're all free",_ and then at the top of the hill walked up Fred, Linda and to his surprise, Kelly. He gave them the Spartan two finger smile gesture and they did the same, but before he could run up to them his radio flared up with the captain's voice.

"_Chief, we have a problem. The covenant are here"._


	8. Chapter 7: you want a torpedo with that?

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 7: you want a torpedo with that?**

Fred couldn't believe his eyes. It was John, he'd come to rescue them. The three Spartans rant up to their friend.

"John it's damn good to..."

John raised his hand to stop him "my ride just informed me that the covenant are here".

"Wait first how did you get in her...?". Fred saw the group of people coming up behind John Two of them were human, wore strange uniforms and carried weird looking rifles. Another one appeared to be a UNSC commander. But it wasn't them who Fred was interested in, it was the covenant elite standing behind them. Kelly and Linda saw it too.

"Covenant" Linda screamed

Fred brought up his assault rifle when john ran up and grabbed his rifle.

What the hell are you doing!" Fred cried.

"Relax, he's with us".

"What, he's the enemy!" said Kelly.

"Listen, you've missed a lot. The short story is the elites have split from the covenant and have allied with us"

It took a few minutes for Fred and the others to accept The Arbiter and with a personal reassurance from Commander Keyes, they set off for where they left Inuyasha. He saw them approaching.

"So who are your friends?" he asked.

"The people who are going to get us out of here, come on we need to get back to the tower" said Fred.

* * *

"Red alert, all hands to battle stations!" Anderson ordered, "tactical analysis".

"Sir, we're picking up 109 ships of various classes. I doubt we will be able to take them all out". Said the ensign manning the tactical.

"Lock phasers on the nearest ship and fire" said Anderson we need to do as much damage to the fleet as possible if we're going to be able to drop shields and beam the away team back.

The _Gettysburg_ turned to face the covenant cruiser and fired its forward phaser banks at the cruiser making contact and drilling all the way to its reactor. They repeated this on two more ships but their shields wouldn't be able to hold out forever against the covenant plasma torpedoes.

--

The _odyssey_, still cloaked, had followed the covenant fleet through the slipspace rift and was was observing the battle.

"Mitchell, we have to help them" said Daniel

"He's right we have to help them" said Sam "from my readings, their shields won't hold up forever".

"I'd sure as hell like to know who they're shooting at first. They don't look like Klingons to me" said Mitchell.

"I can't identify them" said Carter "but their weapons wouldn't be much of a match for our shields considering they're being sured up by the ZPM."

"I can't believe this is happening" said Mitchell, "all right decloak and power up the plasma beam weapons, were actually going to help a star trek ship".

"Indeed" said Teal'c.

--

"Captain ship decloaking off starboard!" said the ops officer.

"Identify that ship" Anderson ordered.

"Configuration unknown, I'm reading human lifesigns aboard though... wait they're hailing us, audio only".

"Put it through"

"_Uh... this colonel Cameron Mitchell of the United States air force ship odyssey, calling the 'star trek' ship... oh oops. did I just call them a 'star trek' ship"._ The captain herd a another voice say _"indeed"._

"Open a channel said Anderson. "This is captain Marc Anderson of the federation starship _Gettysburg_ calling the United States ship, state your intentions"

"_Well, we're kind of lost here and we saw you guys in trouble, so we thought we'd render assistance"_

"If you're sincere we need tactical assistance. That fleet is giving us a hell of a pounding"

"_Uh Rodger that odyssey out"_

"Well that was interesting" said the ops officer.

The captain just sat there pondering about the conversation. A United States ship and they said they were lost. They must be from a parallel universe! But the captain had a feeling that this colonel Mitchell recognized the _Gettysburg_, then there was this 'star trek' he mentioned.

"Captain, one of the covenant ships jumped into slipspace" said ops.

"To where" Anderson asked.

"You're not going to believe me, sir"

* * *

Tarinus looked out from the bridge of his flagship, this new ship was laying waist to the fleet its weapons were as powerful as the new human ship

"Chieftain, I am reading breathable air in the forerunner sphere" said another brute manning tactical.

"Very well, engage the slipspace engines, plot a jump into the sphere. We must recover the reclaimers before the humans do. Prepare to activate the grav beam as soon as we exit and alert the first battalion to prepare to deploy. I will lead them my self".

* * *

The Master Chief and his group arrived at the control tower. Lt Cheney and Inuyasha stayed out front while the others went into the control room. When they got there the chief looked around at the strange group of people, specifically the Spartan-IIIs.

"Fred, who are they?"

"They're Spartans, Chief"

"What! But I thought that you, me, Kelly, Linda and speaking of him, where is Will?"

Linda began to turn away and the other two Spartans stood still. Their expressions where all the explanation the Chief needed.

"Chief" Cortana said breaking the silence "plug me into the master terminal".

"Are you sure about that?" the Chief wasn't taking any chances, not with her.

"I'm sure… yank me".

Kagome was watching as the new group of people arrived then Miroku walked up to Commander Keyes.

"Would you consider bearing my children?" he asked

Sango walked over preparing to slap him but Keyes punched him hard in the stomach. "what the hell is wrong with you! What kind of woman do you think I am" she yelled, walking away.

The Chief removed Cortana's chip, placed it near the console and she uploaded herself into the terminal. A moment later her holographic form appeared over the controls. He turned to see Doctor Halsey standing next to a guy in a trench coat, bifocal glasses and a blue pinstriped suit.

"It's good to see you, John " she said.

The Chief could never forgive her for disobeying orders and taking Kelly when they needed her, but it was still good to see her too.

"Uh oh, Chief" said Cortana

"What is it?" he asked

Then Baker's communicator chirped _"Cheney to Baker, a covenant cruiser just appeared in the sky and it's dropping troops"._

--

Inuyasha had Kagome, Sango and Miroku meet him outside so they could head off the covenant, against the advice of lieutenant Fred and commander Baker. They reached a hill and saw a patrol of four jackals and a brute.

"Killing these demons should be easy" Inuyasha said as he drew his sword and charged.

"Inuyasha, be careful" said Sango "we don't know anything about these demon's capabilities."

He ran up and tried to call the wind scar... but nothing happened. "these demons aren't giving off any demonic aura" he said.

"Ha, pitiful human" the brute said as he raised his spikier and fired. Inuyasha raised his sword and deflected the spikes. He came around and decided to use the adamant barrage; he brought up his sword and swung it, releasing a wave of diamond shards. But they impacted harmlessly on the brute's armor. Then Sango's weapon flew in and killed the jackals, but the brute caught it and threw it off to side. Now it was Miroku's turn, he unleashed his wind tunnel and the brute was being sucked in. But he fired his spikier and one spike got past the vortex, and impacted in his upper chest. He covered up the wind tunnel and collapsed.

"Miroku!" Sango screamed as she rushed to his side after collecting her weapon.

"NOW!" the brute screamed and at that moment a wraith tank rolled up. Inuyasha tried to get to them but it was too late. The tank launched a ball of blue plasma and it hit them in a blast of white light. When it cleared all that was left was a smoking, glassy crater where they were standing. They were gone.

"NO!" Kagome screamed as Inuyasha grabbed her, and sprinted away just as the tank launched another volley.

--

The Chief was still in the control room when Fred got the word the covenant still coming, and they had lost contact with Inuyasha's group.

"All right, Cortana. Time to go" said the Chief.

"No, Chief. I need to stay a little longer. I think I can destabilize the star in the sphere and make it go nova. The blast should take out the covenant fleet which will deal them a substantial blow".

"Ok, we'll cover you". He turned to the Spartans, "Fred, Kelly and Linda you're with me. Arbiter, you better come too".

Fred flashed his acknowledgment light green, he hadn't told john about his promotion but was quite content taking orders from the Chief. He did however bring up one important issue.

"John, we are out of ammo for our rifles"

"Here" Baker said handing Fred a bundle of three hand phasers, he took them and passed two out to Kelly and Linda.

"All right, lets go" said John.

They moved outside and met up with Cheney, then headed off in the general direction Inuyasha went. They found a covenant patrol moving in so they decided to take them out. The arbiter laid down a covering fire as the Spartans and Cheney jumped into they fray. The phasers worked extremely well against jackal shield gauntlets and John was able to finish them with his assault rifle. Cheney took aim and nailed a brute in the face with his phaser rifle and managed to take out two more.

"Just like grandpa taught me" he said.

With in minutes the patrol was wiped out, then a ghost came up. Fred Kelly and Linda set their phasers to maximum, together with Cheney and the Arbiter, they obliterated it.

"Man I love these things" said Fred holding up his phaser.

--

Inuyasha was still holding Kagome as he leaped away from the battle and across the Dyson sphere. She was still crying over what had happened. He finally stopped and he put her down on the grass.

"Kagome, listen. I know how you must feel, but we need to be strong now for Sango and Miroku"

She stayed silent, not even looking at him. They sat for a few minutes before Kirara flew down, carrying Shippo.

"Inuyasha, Kagome we were attacked by those monster things" said the little fox demon as he dismounted "I think the other three got away, but the monsters took the pod things... wait where's Sango and Miroku?".

He paused, how he was going to tell them they didn't make it? Inuyasha just came out and told them what happened. Kirara let out a howl in pain but Shippo just sat there taking in what Inuyasha just said with a blank look on his face. For a little demon, he was able to hide his feelings very well.

"Listen, we need to find the others" said Inuyasha. He helped Kagome onto Kirara's back, then he and Shippo jumped on and took flight, looking for the others.

* * *

"Continue fire!" said Mitchell

The _odyssey_ was maneuvering through the enemy fleet, hitting as many ships as they could in unison with the _Gettysburg_.

"Cam, I've got a lock on those lifesigns" said Carter. "Looks like they're going to have some company".

"Teal'c" Mitchell said, turning his chair to face him "care to take charge of a reinforcement team?".

"I will indeed, Colonel Mitchell" said Teal'c as he walked off the bridge.

"Cam, we have a problem. Someone just entered the computer core room".

"Who was it?"

"Computer records say it was Merrick's ID card".

"Ok, Sam you're with me, Daniel you're in charge"

But before Daniel could object, they had left the bridge. He sat down in the chair and turned to major marks "just keep doing what you're doing".

--

Mitchell and carter arrived outside the door to the core which already had three marines and an engineer standing out front. Mitchell walked over to the comm and keyed it. "Open the door Mr. Merrick. Do you really think we can't just override the door controls".

There was no response and it took Carter only a minute to get the door open. They barged in and Merrick backed away from the console with his hands up. Carter went over to the console to see what he had done.

"It looks like he's programmed the core to build something".

"Can you stop it?" Mitchell asked

"No, we'll have to let it finish"

"What is it?" he asked Merrick who just sat there with a smug look on his face. Mitchell got his answer as it materialized on the pedestal... it was a replicator. But it disappeared in the bright light of a transporter beam.

"What the hell were you thinking!" he said grabbing Merrick by the collar "do you know what it took to kill those buggers the first time!".

"Look around, colonel. The IOA didn't think your plan against the Ori wouldn't work" said Merrick.

"Do you see any Ori outside!" yelled Mitchell.

"Come on Mitchell. This obviously some new Ori plot and those ships are the key".

"_Hey guys"_ Daniel said over the comm _"the ship you just beamed something to jumped away"._

"Take him to the brig" ordered Mitchell.

After Merrick was secured, Mitchell and Carter returned to the bridge

"Status?" he asked marks

"We've take out a few of those ships, shields are holding" he reported.

Suddenly the whole ship shook as a bright orange beam hit the shields.

"What the hell was that!" said Daniel.

"The robot drones" said carter "what ever they used, it drained the shields… a lot".

* * *

Back in the control tower, Doctor Halsey and the Doctor were finishing the plan with Cortana when Ash returned from a patrol.

"The covenant are moving in. We need to leave" he said.

"What about the others?" asked Olivia.

"Tom, Lucy and the Chief managed to get to the rendezvous point. But the covenant got the pods".

"We need to rescue katana" said Olivia

"No, we need to leave now! Cortana has set the sun to go nova, lets get to the rendezvous point, now!" ordered Keyes.

Dr Halsey returned to the console to remove Cortana when she raised a hand to stop her

"No, you have to leave me here. It's the only way for the nova to work". That was a lie, it would work with or with out her, and Halsey knew it.

"Doctor" said Olivia "we need to go"

"Goodbye, Cortana" she whispered as they left.

They had just gotten outside when they were hit by a pair of banshees. The doctor and Donna ran off in the direction of the TARDIS, while the others ran for the rendezvous point. Baker and Keyes took aim with their phaser rifles and fired, damaging one banshee which veered off. But the other kept coming. Suddenly, a missile streaked out of nowhere and destroyed the other one. They all turned to see who had fired it. Six people dressed in military fatigues, one of them holding a smoking rocket launcher were perched on a small him. The leader ran down to meet them, he had a curious golden tattoo on his forehead.

"Greetings, I am Teal'c. We've come to assist you".

--

Inuyasha and his group, what was left of it, landed at the TARDIS just as the doctor and Donna arrived, they all went inside. It was still dark, the Doctor asked what had happened and Inuyasha filled them in.

"There was nothing you could have done" said the Doctor as he removed one of the floor panels near the center console. "Its not here" he said "we can't power up the TARDIS".

"We need to leave now!" said Inuyasha

"And leave everyone else, Doctor we can't" replied Donna.

"I agree. We can't abandon them" said the doctor "but we can't stay here, and without a way to power the TARDIS...".

"Will this work?" said a quiet voice from behind them, it was Kagome and in her outstretched hand was the sacred jewel.

--

Tarinus was leading a flight of banshees when he noticed a blue box in an open field he ordered a strike. But before he could attack a light began to glow on top of it and it slowly faded away, he changed course for the tower his men had just captured.

--

Commander Keyes and her group along with Teal'c were getting acquainted when a wraith tank rolled up. But instead of firing it stopped and john came out of the driver's seat. The remaining Spartans along with the arbiter and Cheney walked up behind him.

"Where is everyone else?" asked the Chief.

"I don't know, we got separated after they attacked us outside the control tower" said Keyes "did you find that silver haired guy?"

"No" said Fred "We found this tank and a brute nearby. If they had a run-in, then its doubtful that Inuyasha and his group survived."

"listen, we got to go now" said Baker

Most of the group started to walk away when John ran up to Dr. Halsey.

"Where's Cortana?"

"John, she stayed behind"

"What! And you just let her", he moved toward the wraith tank and got in but before he closed the cockpit door Fred ran up to him.

"John, what are you doing?"

"I'm not leaving her behind"

"Listen, we don't have time we need to get to the rendezvous point", Fred powered up his IFF tag and when john read it on his display sure enough there was the silver bar of a lieutenant junior grade. "So I can order you not to go, or the commander can". But he didn't.

John closed the hatch and sped off, Fred understood. He wasn't sure if anyone else did, but he knew, John was in love with her. What was he saying, a human and an AI? Sure the Chief spent a lot of time with her, but enough for something like that to happen?

"Fred, lets move it" Kelly said.

He put his doubts aside and ran up to meet her.

"Where's John?" she asked

"He went back for Cortana"

"What! He's crazy, what the hell was he thinking. Do we go back for him?" she asked

"No, we follow our orders" Fred replied.

The two of them ran over to the others, gathered at the rendezvous. Tom, Lucy and Mendez had arrived, Baker and Cheney were setting up three rods in a triangular formation.

"So how are we getting out of here?" Halsey asked.

"You'll see" said Baker as she set up the last rod. "You all want to be in here" baker said as she tapped her communicator. "Baker to Gettysburg, we've set up the enhancers and are ready for extraction, we have a few extra guests joining us. Be advised the Master Chief went back for Cortana, we've lost contact with him".

"_Understood commander. We'll see if we can locate him, Anderson out"._

Everyone stood inside the perimeter and suddenly an energy beam connected the tips of the rods. Fred felt a tingling sensation down his spine as they were beamed away.

* * *

In space, the battle was still raging. The _odyssey_ and the _Gettysburg_ had destroyed 23 covenant ships when the sentinels joined the fray by entering the slipspace field. Most were targeting the covenant, but some began targeting the _odyssey_.

"_Odyssey to Gettysburg our shields are failing, we need to leave now"._

"Understood, you go. We'll send transmit some rendezvous coordinates, and don't worry. I'll see to it that your people are picked up" said Anderson

"_Rodger that, odyssey out"_

The _odyssey_ retreated from the slipspace field, jumped to hyperspace and less than a second later the _shadow of intent _jumped out of slipspace and entered the rift. On the _Gettysburg_ bridge fleet master Rtas Vadum's face filled the viewscreen.

"_Captain"_ the elite said "we detected the loyalist fleet. You had better prepare for docking, also we're picking up increasing energy readings from within the sphere"

"Understood, we need a few minutes to get our people aboard, Anderson out."

"Captain, receiving a message from the away team"

"Patch them through"

"_Baker to Gettysburg, we've set up the enhancers and are ready for extraction, we have a few extra guests joining us. Be advised, the Master Chief went back for Cortana, we've lost contact with him"._

"Understood commander, we'll see if we can locate him, Anderson out. Status on the covenant fleet?

"They're tied up with the sentinels" said ops.

"Very well, drop shields" said Anderson as hit the COM on his armchair. "Bridge to transporter room, start beaming them out"

* * *

The Chief approached the tower in his captured wraith tank, he was lucky most of the covenant were gathered at the entrance. He made quick work of them, hopped out of the tank and killed the brutes standing guard inside. The Spartan dropped his empty assault rifle, drew the phaser baker had given him and stepped onto the platform. In seconds he was back in the control room, only to be met by a brute wearing the armor of a chieftain.

"Ah, a demon! This will be glorious indeed" said Tarinus as he charged toward him. The Chief raised his arm and fired his phaser, taking down Tarinus. What he didn't realize was it was on the stun setting and he was only unconscious. He ran to the master control panel and Cortana appeared.

"Chief, what are you doing! The sun is going to blow any minute, you need to leave"

"Not without you" he said

"Look you need to leave me behind I can't…"

"ENOUGH!" He barked, cutting her off. The Chief reached behind his head, pulled out the chip and held it in front of the console "Cortana, I won't leave you behind… not again, so let's go!".

She looked at him for what felt like an eternity before she reached her hand out toughing the chip and uploaded her self to it. He reinserted it into his armor and ran for the platform. After they got down to the lower level she asked him. "John, why did you come back for me?".

"Later" he said

He walked outside and looked up, the sun was glowing a brilliant white, they were too late it was going to go nova.

"John… I have to tell you something" she said.

"What?"

But before she could say anything they were whisked away by a blue transporter beam.

Anderson along with the UNSC personnel, elites, his senior staff, colonel Mitchell's team and the SPARTAN IIs were in the officers club. They had linked up with the _odyssey_ an hour ago which was riding underneath the _Gettysburg,_ just inside the _shadow of intent's_ slipspace field. He invited Mitchell's team over to partake in the festivities where the captain learned that in Mitchell's universe, the federation and Starfleet were all part of a television show, called star trek.

Fred was standing in a corner; he wasn't comfortable being in a foreign military's officer's club, but the captain reassured him that even though they weren't a part of Starfleet, they were still allowed. It didn't help him shake the feeling of guilt leaving the others behind especially team katana.

The rest of the Spartans and Mendez were getting some well deserved sleep in their quarters, Kelly and Linda walked up to him, both of them had their helmets off.

"Fred, come on and join the party" Kelly said "you're missing all the fun, the captain is talking about his universe".

"Ok, I guess I Will. Say, where's John?" he asked.

"I think he said he was going to a holodeck with Cortana. Whatever that is" said Linda.

--

John and Cortana were on the holodeck running the reach nighttime program. They were both sitting on the grass. He had his helmet off again and she appeared to him in her life-sized form.

"John, there was something I didn't tell you" she started "when I was in high charity the gravemind was able to corrupt some of my base code... which shortened my lifespan. I don't know how much time I have left but I know it's not even a year. That's why I wanted to stay behind. I was going to die anyway".

"I see" he replied

"Why did you come back for me?" she asked again.

I couldn't loose you a second time" he said staring right at her, he also reached out and touched her face. "However much time you have left... I want to spend it with you". John didn't know what compelled him but he leaned his face forward and kissed her. It was weird, kissing a hologram. There was a slight static feel as John pressed his lips to Cortana's artificial ones. When he broke away, Cortana grabbed her head.

"Oh no, it's happening" she said as she collapsed into John's arms.

"Cortana!" he cried, holding her holographic form, trying to wake her.


	9. Chapter 8: betrayals and revelations

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 8: betrayals and revelations**

John was sitting in a chair in the hololab; it had been 10 hours since Cortana collapsed. Her full sized form was lying on a table equipped with a holoprojector. Her program was in a state of suspension, in a way it was like an AI in cryo sleep. Commander Collins along with Dr Halsey and colonel Carter had written a program to temporarily stabilize her system, but this was only a stop gap. It wouldn't prevent a total systems failure. The program needed a another day at least to repair her and bring her back online until then he wouldn't leave her side.

* * *

Tarinus woke up in the medical bay of his flagship; his second in command was standing next to him.

"Chieftain, he said "I am relieved you survived. We managed to rescue you and get away from the repository before the humans destroyed it, but we were able to recover the reclaimers".

"This is good news!" he replied "we will now be able to crush this human scourge and their heretic allies once and for all" he said sitting up and walking for the exit.

* * *

Dr Halsey was approaching commander Keyes's quarters on the _Gettysburg_, she had been wondering how to approach her ever since she saw her on the forerunner instillation. Halsey had of course herd about her death on the ark and she decided it was time for Miranda to know the truth. She walked up to the red double door and hit the call button. She herd a "come in" and Halsey walked inside as the doors parted. Keyes was seated at a glass desk, opposite the couch underneath the view ports.

"Ah, Doctor, its good to see you. Please sit down" she said pointing to the seat opposite the desk.

"Thank you" Halsey said, sitting in the chair.

"I wanted to tell you what a good job you did in the sphere. You really helped, but you might still have to answer for your actions prior to operation first strike. I don't think anyone will care so you're in the clear. Oh by the way, how's Cortana?"

"Fine" Halsey replied "she might be back online by the time we reach Earth. John is still holding vigil at her side. You know, you look like him".

"Pardon?"

"Your father I mean, I uh… I knew him, along time ago".

"Oh I see, he was the only real family I ever had besides my aunt sally. I stayed with her when my father was away on duty. She was his cousin but she passed away a few years ago so... I have no one now".

"What about your mother?" Halsey asked.

"She died giving birth to me".

"Listen Miranda, your mother didn't die in childbirth".

"What!" said Keyes "what are you talking about my father told me that she died".

"No it's the truth. Your father had to tell you that, in order to protect your real mother".

"Who is she then, and why would my father confide in you with this?"

"Miranda" she said slowly "your mother is sitting right in front of you".

Miranda stood up suddenly taking in what she said.

"I see you're not convinced, here" Halsey said, handing her a photograph she removed from her coat pocket.

Keyes took it and looked at it, the date on it was her birth 28 years ago. There were two people in a hospital room. One of them she recognized as her father, he was standing next to a woman lying in a hospital bed. It was Halsey and she was holding a baby. It was her.!

"My mother's name was Miranda, so that's what we decided to call you".

She looked up at Halsey "why did my father lie to me?".

"He lied because he was ordered to do so, otherwise they would have taken you away from us. The deal was that because of my position in the SPARTAN II program. ONI thought if I had any family, they would become a liability and could be used against me by another power. So we had to cover it up, and it was of the hardest things I ever did in my life".

Halsey had tears in her eyes, then Keyes did something Halsey didn't expect she ran up and hugged her and for the first time in a while Miranda didn't feel alone in the world

* * *

Vice Admiral Margaret O. Parangosky was sitting in her office at ONI headquarters holding a file folder and briefing another person in her office. She was pushing 100 years old and held the position of director for almost 50 years.

"Listen up, son" she began "we've intercepted a message from the _Gettysburg_ to lord hood. Apparently, there were Spartan survivors in that forerunner complex on onyx. There were of course SPARTAN IIIs that survived, and now it seems our project is going to be exposed. Ackerson didn't do a through enough job covering up his program so now we're left to clean up his mess. There is also the matter of that AI the Master Chief has, this 'Cortana'. From the reports I've read, she's become a liability and must be taken care of. Am I understood".

"Yes, sir" said a male voice.

"Good. Now our plan is to disable the Gettysburg so you can get aboard. Now in order to get you on that ship we've reversed engineered some forerunner transporter technology recovered from a crashed ship found on Eridanus II. Using this we'll be able to insert your team and get you out before they know what hit them. We also plan to send engineers to recover specimens of their technology. Your secondary objective is to protect my people. But your primary objectives are: to erase any evidence of the Spartan III program, neutralize Cortana, then find a way to destroy the _Gettysburg._ Make it look like an accident.

"I understand, sir"

"Good, dismissed"

And with that the figure encased in SPI armor, turned to leave. Petty officer first class, Timothy-G022, head of gamma company, was about to go into his hardest mission yet.

"

* * *

You wanted to see me, Doctor?" said Anderson, walking into the doctor's office off of sickbay.

"Captain, I was examining our new guests, specifically the SPARTAN IIIs. Take a look" pointing to a display on the wall, he hit a few buttons on his desk and brought up a readout of one of the Spartans.

"From what I can tell their augmentations are pretty much the same, but I found these compounds in their system, this one", he taped some controls and its chemical structure appeared, "appears to be a mutagen that alters their brain chemistry allowing them to tap into their animal instincts during times of great stress or danger. There's also these two", the doctor brought up two more chemicals. "These apparently counter the side affects of the mutagen. I've only found this in three of them, according to the other two Spartan IIIs , those three are from the most recent company. And from my readings, those three are only between 12 and 13 years old".

"What!" the captain said "are you telling me they're kids! But they look like teenagers. What about the other two?"

"They are about 19 years of age, but I'm guessing they went into combat at about the same age as the others. The girl appears to be suffering some form of post traumatic stress".

"It would seem that these SPARTAN IIIs raise more questions than answers" said Anderson.

"Captain, according to my analysis the counter agent is breaking down, it apparently needs to be regularly administered. I've been able to create a retrovirus that will repair the damage done and destroy any traces of the mutagen. I would need your permission to give it to them."

"Is there some kind of risk with these Spartans?"

"Even if they continually get the counter agent, the mutagen will continue to erode the reason centers of their brain. If they don't get the retrovirus then in a few years... they'll be too far gone to help."

"I suppose you have a plan to give this to them?" The captain asked.

I'll have our guests come in for inoculations against Teluvin fever that a member of the crew contracted. I'll give everyone else placebos but the three Spartan IIIs in question..."

"...would get the retrovirus" said Anderson "I'll give you the green light on this doc."

* * *

Tarinus walked into the prophet's chamber and saw retribution sitting in his hover chair, looking at the pod his people had recovered.

"Come, chieftain" he said.

Tarinus walked over to join him; he looked inside one of the pods and saw a human encased in a green armor wearing a helmet with a large yellow faceplate.

"What is the meaning of this!" he said "why are they're humans in the reclaimer's pods?"

"Tarinus, the humans are the reclaimers".

"What! But what you say cannot be true. The forerunners must have made a mistake".

"Silence" retribution yelled "I know how this must sound but gods do not make mistakes. We have been fighting the very species the forerunners left to reclaim their empire. We must seek a truce with the humans. We have defiled the very gods whom we worship".

Tarinus could not believe what he had herd if it had come from anyone but the prophet it would be heresy, and he would have killed them on the spot how he was going to deal with this revelation was anyone's guess.

* * *

John was sitting in the same chair when blue team, Dr. Halsey and Commander Keyes entered the hololab.

"Hey, John" Kelly said walking over and putting a hand on his shoulder "relax, I'm sure that Starfleet program will have her up and about in no time" she said, trying to raise his spirits. But she knew it was no good. They all knew it wouldn't stop her program from degrading, this bought her another month at least. He continued to just sit there, looking at her holographic form.

"John, listen, you need to get some rest" said Fred.

"I'm fine" he replied in a hoarse voice.

"Like hell" said Kelly "even we need rest".

"I won't leave her side" he replied.

"Do I have to make it an order" said Fred.

John knew he couldn't fight them on this so he decided to get some rest and he returned to his quarters the captain had assigned. He wasn't used to such a spacious and luxurious cabin but he wasn't complaining. The spartan removed his armor for the first time in weeks, used the sonic shower, got a meal from the replicator and finally collapsed on the bed. But he couldn't fall asleep, all he could think about was Cortana. John finally dosed off though.

--

The_ shadow of intent _dropped out of slipspace a few hours later, near Cairo station with the _Gettysburg _only. _Odyssey_ had undocked and was waiting at another set of coordinates. They didn't need to surprise the UNSC with another stray ship. The _Gettysburg_ undocked and moved toward the station. On the bridge, Anderson was talking to lord hood about what he had just learned.

"So the covenant want to talk?".

"_Apparently so, their new prophet is contacting us now, I would like for you monitor"._

"Agreed" said Anderson then the viewscreen changed to show the prophet sitting in a levitating chair.

"_You are the leader of the humans?" _he said.

"_No, but I speak for him" _came hood's voice

"_Very well, I have called you because I wish to seek a truce with your people. You may have your doubts but I give you my word we do not have a hidden agenda"_

"_I find that hard to believe, especially coming from you!" _hood said

"_We have realized the mistake we have made we did not know that humans were the reclaimers of the forerunners. Killing the reclaimers is one of the greatest sacrileges of the covenant"_

"He speaks the truth" said the arbiter from behind Anderson "it would seem they have realized their error".

"_And how have you come to this sudden change in judgment?_" said hood

The prophet moved away to revel what was behind him; it was the slipspace field pods.

"_What have you done to them?"_

"_Nothing I assure you, and I will return them I will also accompany them. I will be on a carrier manned by a very small crew, only one ship. Once I arrive we can begin peace talks"._

"_You must understand I need to talk with my superiors"_

"_I do but you must understand that I am coming anyway. What ever you decided to do with me I will not object",_ the channel closed and lord hood reappeared on the viewscreen

"_Arbiter what do you think?" _he asked.

"I believe he is sincere but we should not take the risk"

"I agree with him" said Anderson

"_Well so do I but if there is the slightest chance for peace; I'll have to talk with HIGHCOM, we should still be prepared. Hood out"_

--

John feeling rested enough decided to return to the holo lab but when he got there he found out blue team along with Halsey and Keyes never left, they stayed and watched over her while he was asleep.

"Hey John" said Linda as he walked in.

"What did I miss?"

"Well I'm pleased to report the program will be finished in two hours" said Halsey "she should be back to herself without any trouble, but as you know this will only buy her another month at least".

"I wish we could do more for her" said john sitting down in his usual chair.

Miranda was looking at one of the displays showing Cortana' higher thought process. _"They look familiar"_ she thought to herself, then it hit her. She turned to face Halsey. "Hey I think I just got an idea, we can save Cortana".

John immediately stood up and faced her "if I may ask ma'am, what is your plan?"

"Well from what I understand an AI is created using a human brain, so the AI's higher thought pattern is practically the same as a human neural pattern".

"Ok, just what are you getting at?" asked Kelly.

"I'm saying we use the same process that revived me. I'm saying we make Cortana human".

Halsey looked at her daughter and smiled _"she gets that intellect from me"_ she thought to herself.

"Could something like this be possible?" John asked Halsey, his heart was racing; he and Cortana could actually be together.

"It may require some research but I doubt we have time for that. I'll speak to the ship's Doctor, apparently he's some kind of expert on everything medical" said Halsey

"Well then it's settled. Cortana here is about to become human" said Kelly looking down at her holographic body, still lying on the table.

"_This could actually work"_ thought john

* * *

Tarinus could not believe this was happening. He was there when he presented his proposal to the humans, he knew what he was going to do was right for all covenant.

"Ah chieftain, come in" he said as Tarinus entered the prophet's chambers.

"Prophet, I have herd about your truce with the humans. But is it really true?"

"Yes, it is a wondrous occasion. I will make my announcement to the entire covenant shortly. This will usher in a new age for us Tarinus. Do you understand what this will mean? We may be able to convince the separatists to make peace as well".

"Oh I understand" he said as he drew his gravity hammer. "I understand that you do not deserve to be called a prophet!" he yelled as he swung his hammer at the prophet. The gravitational force caused retribution to be knocked from his chair and on to the floor

"What are you doing, I am a prophet hierarch!".

Tarinus walked over and prepared to swing "No, you are a heretic and you will die as such!" his hammer was the last thing the prophet of retribution ever saw.

* * *

Commander Keyes had explained the plan to lord hood, he was puzzled at first but he agreed to send over the equipment to the _Gettysburg_. They were going to perform the procedure there because the _Gettysburg_ was just so much more advanced. Fred was walking on a corridor on deck 8 when Ash ran up behind him.

"Lieutenant" he said, running up to him.

"Ash, what's going on?"

"Sir, I just wanted to talk to you about my team, I know that we were just temporarily assigned to your team. But I was wondering if we could make it official? I know that my team can help you and you could use all the help you can get".

Fred just stood there looking at ash thinking about what he said, true they were just kids but they've proven themselves in a combat situation before. Which proved what he already knew, they were Spartans.

"Ok I'll talk to lord hood about it, you know we still haven't told him about the Spartan IIIs but I think there shouldn't be a problem. So as far as I'm concerned your officially part of blue team".

"Thank you…" he was cut off as the ship began to rock. Fred thought he herd an explosion. The corridor lights began to flicker and red, flashing strips appeared on the wall.

--

"Report!" yelled Anderson gripping the side of his chair. The science station exploded in a shower of sparks and loose wires were dangling behind him.

"Sir, we were hit by some kind of high speed projectile" said his ops officer, "it cut a hole straight through the saucer. The hole wasn't that big but it went through an EPS relay. We have power fluctuations all over the ship".

"Where did that projectile come from?" yelled Anderson.

"Captain, Sensors indicate it came from an approaching UNSC destroyer. Our communications are also down, we can't call lord hood" said Baker.

"Sir!" Cheney yelled "I'm detecting unauthorized beam-ins all over the ship. We're being boarded!".


	10. Chapter 9: battle of the gettysburg

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 9: battle of **_**the **_**Gettysburg **

Anderson couldn't believe what he was hearing. A UNSC destroyer fired on them and now his ship was being boarded. His Starfleet tactical training instinctively took over.

"Lieutenant" he said looking at Cheney "assemble your security teams, confine all nonessential personal to the safe areas, and hand out phasers to anyone volunteering for security work. Commander Baker, I want to take over tactical".

"Yes, sir" they said in unison Cheney walked over to the turbolift and got in. And baker got behind the tactical station.

"Do we have internal sensors?" he asked ops.

"Negative sir, they went down just after we were boarded. But we counted 22 transports"

So they were dealing with 22 boarders, or more.

"commander, begin counter-intruder program beta-1" this would isolate the designated safe zones with forcefields and lockdown the main computer, it was an order that all Starfleet captains dreaded given because beta-2 was the self-destruct protocol. Anderson hoped he wouldn't have to order it.

--

Fred and Ash were running down the corridor on deck 8 when they bumped into Cheney. He had two other security officers with them, they all had their phasers pointed at ash.

"What's going on?" asked Fred.

"Ask your friend" said Cheney pointing at Ash, "we've been boarded and from what we just herd, the boarders are wearing the same stealth armor as him!".

"What!" said Ash.

Just then Linda's voice came over the comm. _"Linda to Fred, we've been boarded by the rest of SPARTAN III gamma company. Our SPARTAN IIIs are here with us, we're on our way to the armory, is ash with you?"._

"Yes he is, we're on our way, Fred out" he turned to Cheney "proof enough?"

"For now, but you'll explain when we get to the armory".

They met Linda and the other Spartans, except John outside the armory. Cheney typed in the access code on the door panel and the doors opened to revel a large room with weapons, contained in glass cases along the wall. One of them was open and a man wearing a UNSC engineer's uniform was picking apart a rifle. Cheney fired his phaser and it caught him in the back. He collapsed and Linda ran over, looked at him and on his arm was an ONI patch.

"Damn I knew it this op smells of them" she said

"Who?" asked Cheney

"The office of naval intelligence" said Fred "a very shadowy agency, they were responsible for creating the SPARTAN program. Of course some parts of this organization will go to extreme lengths to accomplish their goals".

"Just like section 31" Cheney said, he turned to the SPARTAN IIIs but before he could say anything, Ash walked up to him and began to speak.

"I know what you're thinking, that we're going to turn on you. But we're not mindless solders. We do have a sense of what's right and wrong and frankly, we might be able to convince the others to stop what they're doing. I give you my word that we'll support you".

Cheney turned to the ensign on his left "get some weapons for these Spartans".

"That's what I'm talking about" said Kelly "now we just…" she was cut off as a damaged conduit exploded behind Tom and Lucy. Tom pushed Lucy away but he was flown across the room and impacted the wall, he was alive but he clutched his leg which had a piece of metal lodged in it. Lucy ran over to his side as did Kelly. She looked at the wound. "Fred" she said "he needs medical treatment, fast!".

"All right, you and Lucy take him to sickbay"

"I'll send one of my men with him" said Cheney

Kelly and Lucy helped Tom up and they left for sickbay with a security officer.

"Ok, you got a sniper rifle in here?" asked Linda.

"Here you go, the new prototype" Cheney said as he tossed her a modified phaser rifle, it had an advanced red-dot scope equipped with several vision enhancements.

"Nice" she said as she held the rifle. Everyone else took the standard rifle and Fred grabbed an extra.

"Linda take command, I'm going to get John" he said as he left.

--

"Where's that doctor of yours?" said Kelly as they walked into sickbay finding it empty, they set Tom down on the main biobed.

"I'll get him" said the ensign. "Computer, activate the emergency medical program" he said, then the Doctor appeared out of nowhere.

"Please state the nature of the medical emergency?" he asked.

"Doc, he's wounded" said the ensign.

The doctor picked up a medical tricorder, walked over to Tom, and scanned him.

"So you're some kind of AI?" asked Kelly.

"Yes I am, but unlike your friend I only exist as a hologram. He isn't to badly hurt but we'll need to remove this shrapnel".

The large piece pf metal was lodged in his upper leg. It had missed his knee but removing was going to hurt like hell. Lucy was standing near him holding Tom's hand. Kelly grabbed hold of the metal shard and pulled. Tom cried out in pain then passed out. The doctor moved in, used his dermal regenerator on Tom and sealed his wound, then scanned him again.

"He's lost too much blood we need to give him a transfusion. Ensign, prep the blood synthesizer".

"It's no good doc, all the critical sickbay systems are down"

"Use my blood" said a female voice from behind them; they all turned to see Lucy removing her arm section of her suit. "All the SPARTAN IIIs have the same blood type so we could share blood".

"All right" the Doctor said as he removed a case from a drawer and opened it; it was a field transfusion kit. He inserted one line into Lucy's arm and drew the blood he needed, then removed the line and hooked it up to a line all ready in Tom's arm. Lucy sat down on one of the other biobeds felling light headed, Kelly walked over to her.

"Tell me he's going to be all right" said Lucy

"He should be fine" said the doctor

Lucy removed her helmet and Kelly could see fresh tears roiling down her face, "I thought he was going to die" she said.

Kelly put an arm around Lucy.

"He saved my life" she said very softly "during the war. We were the only survivors. That's why I didn't talk. I couldn't, not after what I saw I care about him, he's really the only one I have left".

Kelly knew what she felt like.

--

John was standing near the table where Cortana still laid. The Starfleet program should be finished soon; he knew that the ship was under attack and the captain's voice came over the intercom saying the _Gettysburg_ had been boarded. There was nothing he could do, he didn't have a weapon and what would happen to Cortana if he left?

"John" came a voice from behind him, he turned to find Cortana sitting up on the table. Her body was glowing a bright blue and the lines of code were running across her body at their usual rate.

"Cortana, how are you doing?" he asked as he walked over to her.

"I'm fine, I ran a systems check. What's going on?"

"The ship has been boarded. I don't know how many there are"

"Then we should get out of here" said Cortana, getting off the table and standing up. But just as she did, the doors to the lab opened to reveal a person wearing SPI armor. The Chief realized immediately that it wasn't one of the ones that he met.

"Spartan-117" he said "you need to hand over the AI"

Cortana moved behind him. "not likely" said john

"I'm under orders to retrieve her by any means necessary" said the Spartan.

"Go ahead and try" replied the Chief.

The Spartan raised his rifle, preparing to fire when another blast of energy his him in his side. He toppled over and fell to the ground. Fred came around the corner and into the room, holding a phaser rifle.

"Nice to see the two of you" he said as he tossed John a phaser rifle he had slung across his back. "We need to get to deck 16. Cheney wants us guarding main engineering in case gamma company makes a run at the reactor."

"All right, let's go" said Cortana

The Chief removed the chip from his helmet and held it out in front of her. She touched it and instantly she disappeared and the chip began to glow blue. He reinserted into his helmet and the sense of cold mercury filled his mind. They then left the room and got into a turbolift

--

Ash was walking alone on a corridor on deck 15, scouting for any sign of Gamma Company. According to what the captain told them, the security teams had isolated most of gamma and a few ONI engineers with forcefields. Gamma couldn't gain access to the bridge to disable them, so the next likely spot was engineering where they could go to shut them off. He knew who was leading the assault on engineering, the best commander of them all. Sure enough when he rounded another corridor, there stood Timothy.

"Ash" he said.

"Tim"

"Well you were the last person I would think to join the other side"

"No, I just joined the right side, unlike you"

"The right side" replied Tim "is that what you call not following orders from the proper chain of command".

"Proper chain of command! That's what you call attacking an ally who helped us in our time of need".

"Orders are orders, but it seems that you've made your choice".

Before he could say anything else, Tim disappeared. Ash ran for the nearest turbolift, he had to get to engineering, realizing Tim's orders if things went south, destroy the _Gettysburg._

--

John and Fred arrived in engineering, he finally got a look at the ship's main reactor. It was three stories high and had red and blue lights running to a main chamber in the middle.

"Whoa!" said Fred as he got a look at it.

John saw on either catwalk was Linda and Mark, their best sharpshooters.

This thing is a matter-antimatter reactor Collins explained we can't let them get near it. This baby could take out the whole ship and anything within a decent sized radius.

Ash ran in and was beginning to tell them about what he learned. When Cortana spoke up

"Chief, I've got contacts approaching!"

Six Spartans dressed in SPI armor came around the corner, firing their MA5Ks.

"Down" Fred screamed as everyone hit the deck, but one ensign was cut down while trying to duck. Chief Collins ran to a panel on the wall and typed in a command. Then a giant blast door slammed shut in front of them. Sealing off engineering from the corridor.

"Well that was close" said Collins, he was wrong. a section of the door exploded and a decent sized hole was present.

"It must have been a Lotus" said Cortana.

The chief wasn't interested, he had bigger things to worry about. Everyone else had been too close to the explosion and was knocked unconscious by the blast, Fred was pinned by a piece of debris, and The Spartans were pouring through the hole. The Chief scooped up his phaser rifle and began firing. He brought down half of them, but by this time the others had their guns trained on the Chief. Then, two shots rang out, it was Linda and Mark. Two of them dropped to the floor and the Chief fired on the last one. But before his blast hit the Spartan, he primed a plasma grenade and tossed it at the core. The Chief was powerless to stop it. But then a phaser blast hit the grenade and vaporized it. The Chief turned to see who had fired, it was Collins. He looked like hell but he was standing.

--

"sir, report from engineering weapons and internal sensors are online" said Baker.

"Good" said Anderson, "Baker scan the ship, see if we got the boarders".

Baker was still manning the tactical station "sir, with the addition of the team neutralized in engineering. We have contained all the boarding parties".

"Good. Beam them to the surface, find a nice desolate area".

"Aye, sir". she typed a few more commands "transport complete... wait, sir. The destroyer is powering up its MAC gun!"

"Disable it"

The _Gettysburg_ fired its main phaser bank and sliced the MAC gun clean of the destroyer. It continued to move toward, but suddenly it exploded.

"What the hell happened?" asked Anderson "did our hit do that much damage?"

"No, sir" reported the ops officer "it looks like a self-destruct. Sir, multiple ships are approaching. Their weapons are hot".

"It looks like they fooled them into thinking we destroyed that ship" said Baker "what are your orders?".

"Helm... set a course for the area where we left the _odyssey_, maximum warp. We can't stay here"

The _Gettysburg_ shot into warp before the frigates could get a lock, but one thing did get through.

--

Anderson was sitting in the observation lounge with his senior staff. He had just gotten the casualty list: 7 dead, 15 wounded including one Spartan. He was weighing his options. 30 minutes ago, Cortana found a message from lord hood embedded in the computer. In it, Hood explained he only found out about the op when it was too late to stop it. Apparently the head of ONI had authorized it. They were supposed to kill or capture the SPARTAN IIIs and terminate Cortana. Then raid his ship and destroy it. Hood had also sent the schematics for the ONI headquarters, he said he couldn't act directly against them so it was up to his ship and the Spartans to stop them.

"Sir, we need to do something" said Cheney.

"I agree with him, captain" said Baker "we need to fight back. We can't just take this lying down, regulations or not".

The captain was standing up, looking out the window at the stars wising by. "I happen to agree with you both but we can't just throw regulations out the window. But these are desperate times. Starfleet never created a regulations about being stranded in a parallel universe and since I've already violated the prime directive, once more couldn't hurt. I've decided to attack ONI. We'll still need time to repair the ship but with the _Odyssey's_ help I think we can do it" he walked over to the table. "Starfleet exists to help those that are in need and to stop those that do harm to others. Its time that we started doing something instead of waiting on the sidelines and watching while innocent people are harmed. I want this ship prepared for battle, Chief" he said looking at Collins, he was worse for wear but the doctor cleared him for duty. "I want that hole in my ship sealed and I want the _Gettysburg_ prepped for combat as soon as possible".

--

All the Spartans were on the holodeck checking out the reach program Cortana had made. She thought they could all use some cheering up considering they were just framed as traitors by ONI.

"This brings me back" said Fred, looking around at the night time sky.

"So you all grew up here?" Olivia asked.

"Yep, they trained us all here. It was the only real home we ever had" said Kelly. She was thinking about everything that had happened, Fred had decided to incorporate Tom and Lucy into blue team and was surprised when Lucy actually said thank you to him. She was sitting with Tom who made a quick recovery thanks to the Starfleet equipment, they were out of earshot of the others but she could only guess what they were talking about. Fred had also mentioned adding one other person to blue team.

John and Cortana were sitting only a few feet away. He had an arm around her and she was resting her head on his shoulder. John had told her about the plan to make her human she seemed excited enough, and she also had her own news to tell.

"John, listen. After you told me about the plan to make me human, Fred approached me with an offer. And I wanted to make myself useful so..."

"Just what did he ask?" said John. He had a fairly good idea about what she was talking about.

"He asked me to become one of you, become a Spartan. And I know what you're going to say but I don't want to be on the sidelines while you risk your life. I want to help you just like always and you could use someone like me someone with my abilities".

"Cortana, I don't want to put you in that kind of danger. I care about you too much".

"John, If I do this. I'll be able to defend myself. I don't want you to choose me over completing the mission. This is my choice, I don't expect you to understand".

"I understand why you're trying to do this... and what ever you decide, I'll support you".

"Thanks, John" she said.


	11. Chapter 10: training day

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 10: training day**

John was standing with the rest of blue team in cargo bay 4, where the flash clone equipment was delivered shortly before the attack. Cortana was plugged into one of the computers and Halsey was reformatting her program for the download. She was also uploading some combat information into her matrix. She would be able to retain this after the download and it would save the time of having to train her in weapons and tactics.

"If only it was that easy for the rest of us" Kelly had remarked earlier.

"Well we're ready. The body has grown to maturity" said Halsey.

John looked into the tank at Cortana's new body, they had used Dr Haley's DNA but it was slightly altered to include the gene necessary for Spartan augmentation. But the face looked exactly the same as Cortana's. She had long brown hair which was floating around in the tank. She was wearing what looked like a swimsuit and attached to her head was a fiberoptic line that led to a neural lace embedded in her brain stem, where the transfer would happen.

"So you can actually grow a complete human being?" asked colonel Carter, who came over to watch the procedure.

"Yes, but we weren't always able to make a complete human. They usually died a short time after, but we've made significant advances since then" said Halsey.

Cortana appeared on a holopad next to the main console, "well the formatting is complete. I'm as ready as I'm going to be".

John walked over to her "are you sure about this" he asked "there's still a risk".

"I'm sure john stop worrying we have the most advanced medical facility on this ship in case something goes wrong".

"its time" said Halsey.

Cortana turned back to look at john, "Look if this doesn't work, just know...".

"save it" he said "you're going to be fine."

She smiled and disappeared off the holopad.

"Do it" he said to Halsey.

Halsey began typing in commands into her keyboard.

"download in progress" she reported. John watched the tank as the fiberoptic cable glowed blue for a few seconds and then disappeared.

"I've got an EKG reading" said the Doctor, monitoring from his own console.

"It looks like the download" worked said Halsey.

John walked over to the tank when Cortana woke up and began to move around violently in the tank.

"Get her out!" he yelled at Halsey.

She typed in a few more commands and the glass door of the tank swung open, spilling its contents on to the bay floor. John caught Cortana before she hit the floor. He pulled the tube in her mouth out and she began to cough up some of the liquid. She opened her eyes and looked up at John, reached out her hand to touch his faceplate but her arm went limp and her eyes shut. The doctor rushed over and scanned her with his medical tricorder.

"She just asleep, Chief. But we should get her to sickbay".

"Alright" he said picking her up and carrying her out of the cargo bay.

--

Cheney was in a turbolift on his way to deck 11. He herd from security that a member of Mitchell's team was caught rummaging through a storage room. Apparently another member of his team arrived and was going to take her back to the _odyssey,_ but not before Cheney had a talk with her, he wasn't contempt to let an attempted theft happen under his nose. He walked out of the lift and ran into two people wearing the same black fatigues, one was a woman with black hair and she was being held by the arm by a taller man wearing glasses he'd met at the party, Dr Jackson.

"Vala if I told you before".

"But Daniel, all those fans would kill to get some actual stuff on that eBay of yours".

"I assume she's our thief, Dr Jackson?" said Cheney.

"Yes lieutenant. Look she didn't know what she was thinking and she's done this kind of thing before so we know how to deal with her".

"Doctor, its all right I wasn't planning on putting her in the brig. I just wanted to make sure she is properly escorted off this ship. But if it will make you fell better, I'll see she's locked away" he said jokingly.

"No I think I've learned my lesion" said Vala to Daniel "and I'm ready to turn over a new leaf and I think the best way to prove myself is for you two to let me go and not send me back to the _odyssey_".

Daniel just glared at her.

"Not working?" said Vala.

"Nope" replied Daniel.

"All right, let's go" said Cheney grabbing Vala's arm as well.

--

John was standing next to Cortana's bed in sickbay. She was wearing a sickbay gown and was on an IV drip. John wished she could just wake up so he could know if it worked. The doctor had confirmed active brain waves, but was it really her? Was it the same AI he had come to know over all this time, all he could do was sit and wait.

"Mind if I sit with you?" said a voice next to John. He turned to see Kelly, still wearing her MK V armor.

"Please" he replied.

Kelly sat down next to him, on the bed opposite cortana's.

"So, she's still asleep?"

"Yeah" he said quietly.

"Hey relax. She pulled through when her program was damaged and she'll pull through again" said Kelly.

"That was different, now she's more vulnerable".

"She's lucky like the rest of us, she'll make it, John"

John finally got his answer as Cortana began to stir. The Doctor walked over with his tricorder and began scanning her, and the chief stood up and walked over to her.

"Doctor" she said very groggily "why do my eyes hurt?"

"Because you've never used them before. Try and relax I'm sure this is a strange experience".

John took off his helmet and looked into her eyes.

"John?" she said

"Yes, I'm here"

"This is all very strange" she said "its like... well to tell you the truth. I can't really describe what it's like".

"Its ok, just try and take it easy" said John.

"Say Doctor, when can I leave?" asked Cortana.

"Now if you like. But don't strain yourself. Your system doesn't need another big shock... oh before you go". He came over and pressed a hypospray to her neck. "This is a stimulant and some anti-nausea medication, so you can stay up and about".

"Good" she said as john helped her off the bed "now where can I change into something a little more comfortable".

"Of course, there's a room over there" he said pointing her to the doors on the other side of sickbay.

"I'll give you a hand" said Kelly and she helped her into the room.

--

Anderson was inspecting the chief's repair efforts. He was lucky that the _shadow of intent_ arrived with those engineers of theirs; they were the strangest creatures he'd ever seen but they got the job done. He walked to the hole and looked down, the hole itself was probably only 500 ft long, but it blasted through 6 decks. Inside the hole covenant engineers and his own people using thruster packs, were trying to seal the breaches. More extensive repairs would have to be made at a starbase, assuming they make it back.

"Captain" said Collins who came up behind him "this is amazing. I mean these engineers really know their stuff".

"Listen Chief, I need this made as soon as possible" he said, handing him a padd.

Collins looked at it, "captain, are you sure about this?".

"Positive. Get it done ASAP".

--

John was in the mess hall with Kelly and Cortana. She had changed into a gray jumpsuit and Kelly helped her get her hair into a pony tail. The Doctor suggested she eat something and Cortana was happy to comply, over the last hour she tried 10 different meals.

"You should take it easy before you get sick" said John.

"I know" replied Cortana with a mouthful of spaghetti "but this is all so good and the Doctor said I should eat something to keep my strength up. I still have to make it through augmentations".

John had almost forgotten about the plan. He was worried he saw what happened to the other candidates, the ones who didn't survive and the ones who were deformed or crippled, he didn't want that to happen to her.

"John?" said Cortana.

"Yes"

"You all right? You look like you've got something on your mind".

"It's nothing".

"_Anderson to master Chief, I need to speak with you" _

"On my way" he said. He turned to Cortana. "I'll see you later".

--

The Chief arrived in the observation lounge a few minutes later. In there was the captain, Commander Keyes, the Arbiter and the _odyssey_ commander col. Mitchell.

"Chief, the colonel here needs to bring us up to speed on something".

Mitchell began to explain what Merrick had done at onyx and what the replicators were.

"Reminds me of the flood" said john when Mitchell finished.

"Who?" asked Mitchell.

"You don't want to know" replied the Spartan.

"Anyway" continued Mitchell "Carter was able to figure out that the IOA must have put in a fail-safe in order to make sure that the replicators wouldn't come back to our galaxy and they probably told Merrick what it was. Carter is having no luck finding the code her own".

"Captain, I have an idea" said the Chief "but you're not going to like it".

* * *

Mitchell was outside the brig on the _odyssey_ with "Teal'c and their guests.

"Ready" he said to Teal'c.

He nodded and Mitchell opened the door and they both went inside and Mitchell shut it behind him. Merrick was leaning on a wall with his arms crossed and the same smug look on his face.

"So" he said "you finally decide to interrogate me. I read Teal'c's profile and his methods won't work and like I said Mitchell. I used to do what you did, so you wouldn't make much of an interrogator".

"Oh, I never said anything about us interrogating you" said Mitchell who pulled out a remote and clicked it causing the brig wall to retract up into the ceiling. On the other side stood the Arbiter and the Chief in his armor. When Mitchell looked back at Merrick he saw what actually looked like a look of concern on his face. He walked over to him and whispered in his ear "these two are from this universe the universe you screwed up by unleashing your IOA science project, and you'll wish that Teal'c had interrogated you after these two are through with you." He walked back over to Teal'c "Well I'll leave you three to get acquainted" he turned to John and whispered "he's all yours chief". Mitchell and Teal'c started to leave when Merrick finally broke.

"Wait! Ok I'll tell you".

"Now it seems you three aren't getting quality time" said Mitchell "ok spill it".

"I was told that the shutdown code was on the other side of the crystal I inserted into the core".

"Now isn't easy when you just cooperate" said Mitchell as he left and shut the wall behind him he turned to the others.

"Now all we need to do is infect the replicators with this code, but we need to find them" said Teal'c.

"First we take care of ONI" said john "then we can find these replicators of yours".

"I think we'll run into them before too long" said Mitchell.

* * *

Commander Adams was on the bridge of his frigate, the _midway._ They were assigned to hunt down the _Gettysburg_ after it destroyed a UNSC ship and fled Earth. Why they did it was on his mind, but that didn't matter. ONI's orders were clear: destroy the _Gettysburg_.

"Sir, I have a contact" reported his tactical officer "it's a covenant CCS class cruiser. But scanners are picking up strange readings… wait it's powering up weapons!"

"Alright, load a Shiva and fire", the captain knew it would take too long to power up the MAC gun and archer missiles wouldn't do enough damage. He needed to take them out before they took him out.

"Missile away, sir"

"Alright back us off"

The _midway_ fired her engines and darted away as the covenant ship was enveloped in a bright white light, and disappeared.

"Report" asked Adams.

"Sir, the ship has been completely destroyed but I am picking up some debris that doesn't match any known covenant alloys".

"Let's get a sample and we'll take it back to Earth for those ONI scientists to drool over. At least it'll get off this damn patrol".

* * *

John walked into the briefing room on deck 10 where the captain had assembled everyone. Anderson walked in and looked around. In addition to the captain and his senior staff. There was col. Mitchell's team, SG-1. Commander Keyes and the Arbiter with Rtas vadum. Fred was also there as head of blue team. The captain asked everyone to sit down and they got down to business. They had their attack planned out, the _Gettysburg_ and _odyssey_ would keep the space forces busy while the Spartans, along with an elite task force and SG-1, would launch an assault on ONI HQ. It was a good plan but things were bound to get hairy on the surface and they would need heavy support. They planed to attack in 3 days which gives them enough time to train Cortana and repair the _Gettysburg_, but even if the attack succeeds they still had these replicators to worry about.

"To minimize casualties we've also modified our phasers to send out an EM pulse so when we hit a UNSC ship with our phasers. It will disrupt their computer systems and disable them" said Collins.

"There's still the prowlers" said Keyes "they're run by ONI and they're stealth ships. I don't know if you'll be able to detect them and they usually carry nukes".

"We have a plan for that" said Anderson.

"I will have a small force transferred to the _odyssey_" said the arbiter "from what I understand your ship is equipped with a new type of cloaking device that renders your entire ship invisible".

"Well you heard correctly, Mr. Arbiter" said Mitchell.

"Very well then" said Anderson "Lieutenant Fred, ask Commander Collins if you need anything, dismissed".

"I do as a matter a fact" he walked over and asked about replicating a set of armor.

* * *

Lord hood walked into his office in Cairo station, he had been in seclusion for the better part of two days since the Gettysburg was forced to run. He could only hope his message got through. He sat down at his desk and opened a file folder which had a report about a frigate destroying a covenant cruiser. Hood just started to read it when he heard a strange noise and looked up to see a blue box had appeared in his office. It looked like an antique phone booth with the words **police public call box** on the top. Then its doors opened and four people stepped out.

"Hello, I take it you're in charge here. I'm the Doctor, I'm a friend of a lieutenant Fred. Do you know him, he's a big fella in a green suit?"

"Yes I know, him and you must be 'the doctor' he mentioned".

"Yea listen, we came to see if they made it out alive" said Donna.

"They did, but they're in trouble" he proceeded to tell the doctor's group what had happened.

"So now you need our help?" said Inuyasha.

"Correct, like I said. I don't know if they got the message but I'm sure they did, either way they need help. I can't do anything without raising questions and I'm already suspected of trying to help them. I do have a plan to help them but it only goes so far".

"Look we'd love to help, but there's only four of us" said Inuyasha.

"Hey Doctor, I think I got an idea" said Donna "but you're not going to like it".

"What is it?"

Donna walked over and whispered in his ear.

"Oh come on do we really need to involve them" said the doctor "I'll have to owe them one and they'll bring me on some alien hunt across the countryside".

"Doctor we owe Fred and his team" said Donna.

"Could someone explain what's going on?" asked hood.

"Sorry, any way we may be able to help you after all" said the doctor "although I don't exactly agree with the plan".

"Ok we'll need to coordinate efforts" said hood.

"No need. Here take this" the doctor tossed him a small device.

"Its a transmitter, just turn it on and I'll get the message, any way we need to go and get some help". With that the four of them went back into the TARDIS and closed the door then it disappeared. Hood returned to his desk and sat down _"that was the strangest group of people I've ever met"_ he thought to himself _"but could they really help?"_

* * *

John walked into his quarters. "_I've had a long day"_ he thought to himself. But he got a surprise when he found Cortana waiting for him. But she was different, she got a hair cut. It looked just like her old hairstyle when she was an AI, long in the front and short in the back, even her hair color was blue.

"Do you like it?" she asked "I had Dr Halsey cut it for me. You know I guess she's sort of my mother now".

John was speechless, she looked beautiful even though all she was wearing that same gray jumpsuit. "it looks good" he finally said.

"I'd thought you like it" she replied.

Cortana walked over to him and removed his helmet "listen, John..." she started, he noticed she was starting to blush. "I was wondering about us? Our relationship?

"What about it?"

I was wondering if was ever going to lift off. Now that I'm human, I can be there for you... in 'that' way"

oh, I see said John.

Cortana wrapped her arms behind John's neck and kissed him. Her hands wandered to the release latch for his MJOLNIR armor.

--

John was sitting on the bed while Cortana was asleep next to him. He couldn't sleep, all he could think about were the augmentations. They were going to be performed today in a few hours. _"Will she still be the same he thought to himself?" _Then he remembered what Kelly had told him _"She's lucky like the rest of us, she'll make it"._ All of the Spartans had their fair amount of luck, she would need it.

* * *

Lord Hood was sitting in his office when his secretary walked in with the usual messages but when hood sifted through them one caught his eye in particular

_**Longstreet's forces will attack the little round top in two days. We'll surprise the union forces from behind. **_

The sender was unknown but hood knew who it was from.

"_They got it"_ he said to himself

* * *

John was standing in the corridor outside the med lab. He couldn't watch anymore, Cortana was lying on the table with all those needles poking her. The doctor could only give her a light sedative but apparently that didn't stop the pain. They had to use replicated UNSC equipment for the procedure because the doctor said "no one in the federation had done a procedure like this before". And using Starfleet equipment would be too risky. Cortana left the schematics for the equipment in the ships computer so they could replicate it. He was watching it all happen from an observation booth in the lab. The procedure was bring up some bad memories, he remembered the pain when they stabbed that needle into his bone marrow and how his skin felt like it was on fire.

"Mind if I join you, Chief?" came a voice from behind him. He turned around to find Captain Anderson standing right there.

"Not at all captain" he replied.

"So what are you doing in the hall?"

"I couldn't watch, it was reminding me of some past experiences".

"You mean your own augmentation".

"Well... yes. During the surgery half the candidates died or were crippled. Me, Kelly, Fred and Linda are the only ones left out of those who made it through all right. Everyone else was killed during the war".

"Believe it or not, I know how you feel. I lost most of my crew during my first command... and that was also during a war".

John was surprised "I thought that your federation was dedicated to peace?"

"We are, but we were invaded by a hostile race from across the galaxy, called the Dominion."

The captain and John spent the next hour trading war stories until the doctor came out of the lab and John rushed over to him.

"Tell me she's alright?"

"She's fine, Chief. We just transported her to sickbay to recuperate. You can go and see her if you like".

The chief immediately left for the nearest turbolift.

"So how's our attack plan going?" the Doctor asked the captain

"Well we sent a message to lord hood, we just have to hope he gets it. And Collins should be just about finished with our 'little surprise'."

--

John walked into sickbay and saw Cortana laying on the same biobed asleep. She looked pail and week, even though she was now stronger than most of the people on this ship. He sat down on the same biobed as before and continued to watch her.

"Déjà vu" said a voice from next to him, he turned to see Kelly.

"It looks like she'll make it once again" said Kelly "that's a good sign she'll make a good Spartan, John".

She was out of danger for now but could she really handle herself in a fight.

"John" came a quiet Cortana. "Ugh, I feel like crap" she said after trying to sit up only to fall back against her pillow.

"Take it easy. The Doctor has pumped your system with a lot of drugs, he says it will accelerate your recovery" said John.

"When will I be up and about?" asked Cortana.

"He says later tonight, but don't expect more rest. We need to get you outfitted with your armor. I need to check in with Commander Keyes, let her know your augmentation went smoothly. I'll be back later".

--

Keyes was in the observation lounge with the captain and col. Mitchell.

"Captain, we need someone to command the odyssey?" said Mitchell "none of our officers are experienced enough. I was wondering if you had an officer who could do it?"

"Well I need Baker with me, but I think I have a more suitable candidate", he turned to Keyes. "well how about it commander""

Keyes was a bit startled _"am I ready for command again"_ she thought to herself _"well on the other hand I've just been nothing but ground infantry since this whole thing started"._ "I'll be glad to" she finally replied. Just then the Chief walked in

"Commander, Cortana's augmentation went perfectly, no side effects"

"Good" she replied "we were just hammering out the final details of our attack plan. I hope you have your own insertion plan in place because we can't beam you down".

"I do ma'am, commander Collins has been helping me out".

"Oh and speaking of him" said the captain "he said that he's finished replicating that armor you wanted, and its waiting on the holodeck".

"Thank you, captain" the Chief said as he left.

--

Cortana walked into the holodeck with John a few hours later. The program they were using was one that Fred had cooked up for her. It was a UNSC training facility complete with a firing range and an outdoors obstacle course. When they went in it was all ready activated. They were in the armory and in the center of the room was a brand new set of MJOLNIR Mk. VI armor. Collins had offered to replicate Kelly a new set but she declined, she said her old Mk. V had gotten her through tough spots.

"I never thought I would actually wear one of these things" said Cortana as John helped her into the armor.

"It's a shame that Chief Mendez left the ship at Earth. He would have made a better trainer than me" said John.

"Oh I think you'll do better than him" replied Cortana.

It took them 45 minutes to fit the armor on but once they did Cortana was immediately off to the firing range. She hefted a MA5C and she immediately knew how to load and fire thanks to the upload.

"It's strange, its like I've done this before" she said

They tried several weapons over the next fifteen minutes. Cortana seemed partial to the M7 and the BR55 so they stuck with it. They practiced a little hand-to-hand sparring then they moved to the obstacle course. John activated a standard ring the bell scenario using the holodeck controls. Cortana was able to run fast enough to avoid most of the bullets fired from the training guns. She ducked behind a pillar and brought out her SMG, then let loose a barrage right in the gun's processor circuits and it shut down. Cortana took out a frag grenade and threw it at the other gun which landed right under its tripod and exploded, she moved on.

"So this is what he had to go through" Cortana said to herself, remembering when they first met and the near fatal training run they did. She darted forward and continued toward her objective, that's when John decided to mix things up a little. Cortana looked up to see a hornet flying towards her.

"Oh now why did he have to give me a hornet?" she said.

Cortana quickly formulated a plan, she climbed up one of the poles and looked over at the hornet.

"I've got to time this right" she said. She brought out her battle rifle and looked down the scope. "There!" She said as she eyed the small forward intake. She pulled the trigger and let off four, three round bursts into the intake. This caused the engine to fire forward and that was her chance. With all her strength, she pushed off from the pole and landed right on the hornet cockpit. The holographic pilot seemed surprised at first, then he went for his sidearm. "Sorry but no" Cortana said as she punched her fist straight into the windscreen and continued into the console, which exploded in a shower of sparks. Immediately, the engines seized up and died and the hornet began to fall. Cortana jumped off just before it crashed and exploded. She landed with in a few feet of the bell, got up and sprinted toward it. Finally she felt the cord in her hand and she rang the bell.

"BRAVO!" someone called and she turned not only to see John, but Fred, Kelly and Linda were there as well.

"Well I think she's ready" said Fred.

"Definitely" said Linda.

"Well then its settled. Welcome to blue team, Cortana" said Kelly.


	12. Chapter 11: endgame part 1

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 11: endgame part 1**

Fred was with John, Kelly, Linda and Cortana on their way to the shuttle bay. John said he'd been working on a plan on how they were going to get to ONI HQ.

"So what have you been cooking up?" said Fred.

"You'll see" replied John.

They arrived outside the door to the shuttlebay "you're going to love this" said john as the doors opened they walked into one of the three alcoves in the back of the bay. Fred was surprised to find a pelican dropship, but there was something different about it. The pelican's usual armor had been replaced with a silver colored metal.

"Well, what do you think?" said John.

"First where did you get it? And second, what's that stuff on the hull?" said Linda.

"We salvaged it off the_ forward unto dawn._ Along with some other equipment before we came back to our universe" said Cortana.

"I asked the Chief engineer to refit the pelican with some armor alloys from his universe" said John "and prepare a few other things." He led them over to a table and on it were 5 MA5C assault rifles, 5 B55s and 3 M7s and Linda's sniper rifle.

"I don't get it" said Fred.

"Maybe I can explain" said Chief Collins who came over from the pelican. "We installed a micro replicator in the bottom of the magazine. It will replicate a new round every time you fire off one".

"Essentially, its infinite ammo" said john.

"Now that, I like" said Linda picking up her rifle. "Hey there's some new vision modes" she said looking down her oracle scope. Fred and Kelly each hefted one of the MA5Cs, when the ammo counter was activated, it displayed the symbol for infinity.

"Nice touch" Kelly said.

"You should check out the pelican" said John as he led the Spartans over to the dropship. "The engines have been replaced by Starfleet ones. And they put in an inertia damping system, so we'll be able to handle high velocities".

"We're going to need all that speed to break through the defense perimeter" said Cortana.

They looked inside and were surprised to find all the Spartan IIIs working inside it.

"Hey el-tee" said Ash as he ran out to join the Spartans. "the Master Chief asked for our help on his plan. He told us not to tell you, wanted it to be a surprise".

"Well you did good, petty officer" Fred replied.

"Thank you, sir"

Just then the captain's voice came in over the intercom _"red alert, all hands to battle stations. We'll be arriving at earth in one hour"._

"Blue team, prepare to move out" ordered Fred.

* * *

Keyes was on the bridge of the _odyssey_ looking out over Earth. The _odyssey_ had flown ahead of the _Gettysburg_ and was observing the UNSC forces under cloak. Colonel Mitchell got up from his seat and walked over to the commander.

"Nervous?" he asked.

"You could say that. It just, this is the first ship I've commanded since I came back".

"Relax, you'll do fine said Mitchell "this ship has been in worse situations. It'll get the job done".

"Thanks" she replied

"Cam, the _Gettysburg_ will be arriving in a few minutes. we need to get down to the hanger" Carter said from behind him.

"Well commander, you're in command" said Mitchell as he left the bridge. Miranda walked over to the command chair and sat down. She had to admit this was cool, she was commanding the most advanced ship she ever saw, besides the _Gettysburg_.

"Ma'am" said major Marks "the phantoms are standing by in the hangar"

"Good, we'll launch them as soon as the_ Gettysburg_ arrives"

She looked out of the view port at the fleet of UNSC ships. There were 55 destroyers, frigates and cruisers. More than enough firepower to decimate both ships, but with a little luck they might survive this whole mess.

"Ma'am" said the female lieutenant on her right "the _Gettysburg_ is dropping out of warp".

"_This is it"_ she said to herself "major, sound battle stations and prepare to decloak the ship".

--

Anderson was on the bridge of the _Gettysburg_, they were all anxious about the maneuver they just pulled off. Dropping out of warp close to a planet was dangerous, but it was the only way to avoid the fleet and to catch them off guard.

"Report?" asked Anderson.

"Sir, it looks like we pulled it off, but the fleet is coming about".

Alright, fire the low yield torpedoes. Set for proximity detonation. Lets see if we can shake them up a bit.

"Aye, sir" said Baker who was once again running tactical.

* * *

Commander Adams watched from his frigate as the torpedoes left the _Gettysburg_ and detonated in-between several ships, his included.

"Report?" he asked as his ship shook violently.

"Sir, no significant damage reported and the same goes for the fleet".

Adams was wondering why they didn't destroy them, they had the firepower.

"Sir, new contact, unknown classification"

"What!"

He watched as the new ship shimmered in and began firing blue beams of energy at the fleet. But their strikes didn't destroy the ships

"what's it doing?"

"Sir, the targeted ships appeared to have lost main systems. The same thing appears to be happening to the ships the _Gettysburg_ fires on".

"We still have to stop them. Arm missile pods A5 through B3 and get a solution for the MAC gun".

* * *

The _odyssey_ and _Gettysburg_ had disabled 11 ships and the opening salvo of torpedoes had damaged 2 others. But now the _Gettysburg_ was avoiding missiles and getting skimmed by MAC slugs.

"Shields at 92 percent" reported ops.

The captain taped a button on his arm panel. "Chief, you have a go".

--

"Aye, sir" said the Chief, standing in the pelican's cockpit. Cortana was at the helm. "Take us out".

"You got it" Cortana said as she fired the pelican's new impulse engines. It darted out of the bay, passed through the shields and headed for Earth.

"Its amazing we're not pulling any gees" said Kelly in the troop compartment.

"Well don't get used to nice feelings. We're going right into the thick of it, get ready" Fred ordered. And with that, blue team got up and checked their weapons.

"We're one minute away" said Cortana from the cockpit.

"Well that was fast" said Ash as he donned his parasail. Their plan was two split up blue team into two squads. The Spartan IIIs would use parasols to insert on the roof and the Spartan IIs would go in the front door.

"This is it" said Fred as he hit the control panel and popped the hatch "go!".

Ash and his squad jumped from the pelican and began their free fall.

"_Alright, on three, open your chutes then head for the roof on the north wing"_ Tom ordered.

Ash winked his acknowledgment light green.

"_Ok, one… two… three" _

Ash tugged his cord and his chute opened. He looked around and saw four other chutes

"_ok, let's head for the roof"._

--

"Hang on!" said Cortana as she pulled some evasive maneuvers in order to avoid some SAMs fired from ONI HQ. John was in the seat behind her and he activated the pelican's two missile pods, targeted the SAM sites and the main power lines. "Here goes". He pressed the trigger. All of the pelican's Anvil-II missiles streaked away and struck their targets.

"direct hit" he said "ok Cortana, take us down".

"aye, aye" she said as she brought the pelican down and landed in an outer parking lot "

"Ok let go" said John as he and Cortana got out of their seats and grabed their weapons and joined Kelly, Linda and Fred who were waiting outside.

"lets end this once and for all" said John as they began walking toward the concrete gate.

--

Dr. Hyer was in the science labs at ONI analyzing the specimine that the frigate _midway_ brought back. It looked like some kind of spider, comprised of blocks made from an unknown alloy. They had isolated it in a transparent box and it was energized with an eletrical field. He had been told that it actually tried to escape, and the field had stoped it.

"Well you're an interesting one" he said looking at it and just then main power cut out.

"Oh hell" said Hyer as he fumbled around in the darkness. Then emergency power kicked in and then lights came back on. But when he looked back at the spider it was gone and there was a hole in the box. It looked like the glass had been melted. "where is it?" he said to himself. And then he got his answer as it droped from the celing, onto his face and sprayed him with the same caustic substance.

"AHHHHH!" he screamed as he fell backward, but his hand hit the alarm button on the console.

--

Timothy and his team were on their way upstairs to the roof. They had detected 5 signals heading for the roof and his squad was sent to intercept them. Just then he got the report of the alarm in the lab complexes.

"Continue to the roof" he ordered as went down two floors and emerged into a coridor. But the walls looked like they had been chewed away by something. Then sudenenly, he herd this weird metal clanking sound comeing from all around

"Be advised" he transmeited on the ONI frequency "lab coplex has been comprimised by unknown force". He looked up to see several replicators on the celing. He fired his assault rifle at them and managed to destroy a few, but they just kept coming. Two of them jumped on to his back and they swarmed over him.

--

Ash was still in his decent when he saw movement on the roof.

"Phasers" he called out to his teamates, they pulled out their hand phasers and turned on the widebeam mode. They fired, covering the entire roof with a stun field. Then landed only seconds later They shed their chutes and policed the other spartan's weapons. Ash reconized them as Tim's squad, but where was Tim?

"Ash, lets go" said Tom he ran over to the door and they went down the stairwell but Ash stoped when he reached the door to the lab level.

"Hang on Tom. I'm going to check something out"

He got a green acknowledgment light, he walked into the coridor and immedately noticed the walls. But when he looked down he saw an assault rifle lying on the ground surrounded by spent shell casings. He herd a sound coming from down the hall so he went to investigate. Ash walked into a large lab and that's when he saw a replicator on one of the tables. He took it out with no difficulty but when he turned to leave he saw Tim standing in the doorway, but there was somethind wrong with him. His helmet was missing and his face seemed swolen on one side. His SPI armor was also torn up. Ash soon discovered the cause, two replicators were imbedded in his back, their legs implanted in Tim's skull.

"What the hell" he said.

--

"DOWN" Fred screamed as a grenade detonated over their heads. The spartans dived behind a concrete barrrier. They were almost to the doors when ODSTs began pouring out guns blazing.

"There's too many of them" screamed linda. Then they saw a line of scorpion battletanks rolling down the road they just came from.

"What now?" said Kelly.

Then they herd it, that strange sound. And they looked up to see some kind of ship materalizing in mid air. The spartans didn't know what to make of it. It looked like some kind of carrier but it had engines on either side that pointed down.

"Its some kind of atmospheric carrier" said Cortana. Then a loud voice came from the carrier, the speaker had a british accent.

"_Attention all ONI forces. This is the UNIT carrier valiant, throw down your weapons now!"_

The solders continued firing but the scorpions turned their turrets upward.

"_Well have it your way"_ came a familiar voice. Then a bright green beam left the valient, hit the scorpions and obliterated them.

"Nice save" cried Fred.

"You ready?" asked John.

They all flashed their acknowledgment lights.

"Ok, let's go" said john as he and the other Spartans hopped over the barrier and charged at the ODSTs.


	13. Chapter 12: endgame part 2

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Chapter 12: endgame part 2**

"Continue fire" said Anderson. The _Gettysburg_ was maneuvering between the UNSC fleet at high speed. It was very risky but it kept them from hitting the _Gettysburg_ with their MAC guns and they managed to take out some ships as they went. But it was only a matter of time before the fleet regrouped. The _odyssey_ was fairing much better considering they had a ZPM boosting up their shields.

"Captain the UNSC fleet is regrouping and they're fir…" Baker was cut off as the ship was rocked by MAC slugs hitting the shields. Sparks shot out from the display behind Anderson.

"Report?" he yelled

"Shields at 45 percent, aft torpedo launchers are down" said Baker.

"Ok I think its time to deploy our special surprise" said Anderson.

"Aye sir" said baker she tapped a few controls and outside the ship a plan they borrowed from voyager went into action. Holo emitters positioned on the _Gettysburg_ hull projected the image of several federation starships which got the UNSC fleet panicking.

--

"It worked" said Keyes looking out of the bridge of the _odyssey_

"Ma'am" said marks "I'm picking up intermittent contacts"

"The prowlers!" said Keyes "contact the _Gettysburg_, now!"

* * *

The Chief and the other Spartans continued their forward charge at the line of ODSTs. The helljumpers continued to hold their ground and they waited for the Spartans to get in range. But they never got their chance as a bright yellow energy beam struck them and sent several ODSTs into the air. The Spartans looked to see who had fired the beam and they saw Inuyasha landing next to them, holding his sword.

"How the hell did you get out of the Dyson sphere and where did you get that ship?" asked Fred.

"Long story" replied Inuyasha "hey, I only thought there were four of you" he said noticing Cortana.

"New member" said John.

Then two phantoms decloaked right above them and their gravbeams came to life. Out of one came the arbiter's team and SG-1 and from the other came a pair of hunters and Cheney's security team. A V22 osprey landed and UNIT commandos along with Kagome and the Doctor came out.

"We thought you could use a hand" said Mitchell.

"It's much appreciated" said Kelly.

"Rockets" screamed Linda as they looked to see some of the ODSTs hefting jackhammers.

"Behind the hunters" said John as the two massive creatures moved to take point raising their shields hoping to deflect the rockets. But there was no need a bright purple light hit the ODSTs and it stunned them all.

"Well that was easy" said Kagome holding her bow.

"Spartan, we'll remain outside and make sure no reinforcements come" said the Arbiter "this is your fight".

"Thanks" said John and the rest of the group proceeded to the main entrance but a titanium-A blast door had shut over the entrance. The doctor ran to an access panel, pulled out his sonic screwdriver and pressed it to the panel, then the door retracted.

"Let's move" said John as the Spartans and SG-1 proceeded inside.

--

Ash brought his assault rifle up and fired three shots into Tim's legs, but he didn't even flinch. He shot him once in the chest, same result. Then Tim grabbed Ash's rifle, pulled it free of his hands, and broke it in two.

"Well we'll have to do this the hard way" said Ash as he prepared to fight hand to hand. Tim hit him across the room with one hand before ash could through a punch.

"Ok that was unfair" said Ash as he got up. But before he could regain his posture, Tim rushed him, kicked him hard in the chest and Ash was once again on the ground. He could taste blood in his mouth and from what he could tell, he had cracked a few ribs.

"Ok no more mister nice Ash" he said as he got up, lunged at Tim and kicked him in the chest, but he didn't move. Ash followed up with a few punches to his face but no luck, he took every one of them. Tim grabbed Ash's fist and head butted Ash in the head, shattering his helmet's visor. He picked up Ash and threw him across the room. He hit the wall on the other side but he got up immediately and coughed up some blood. Then in a flash Tim had darted across the room, grabbed Ash's neck and pushed him up against the wall. Ash could feel his windpipe being squeezed, he had to act fast so he reached around with his hand and pulled out one of the replicator legs stinking inside Tim's head. Tim's grip relaxed and Ash fell down on his feet.

"Ash?" he said.

"It me, Tim"

"Listen, you need to kill me"

"Hold on, Tim. We'll get those things out"

"NO!" he yelled "you need to kill me. I'm too far gone and I saw what their going to do, you need to kill them all. You need…." He was cut off as Ash herd a squishing sound, the leg reinserted in his head and the replicators took control. Ash stood up and prepared to fight but then he herd a familiar voice scream "ASH, GET DOWN". He ducked in time to see the rest of his squad open up with their assault rifles on the altered Tim, but no luck. Then Ash saw a plasma grenade on Tim's belt. He summoned all his remaining strength, reached out and primed the grenade. It began to glow blue. "RUN!" he screamed to his teammates as he got up and ran for the exit, but the grenade went off. Incinerating Tim and the concussive force sent Ash flying into the wall. He was in and out of it but he saw Mark and Olivia pulling him out.

--

John and his group made their way through the halls of ONI when they herd a very strange sound which SG-1 recognized.

"Oh crap" said Carter. Then they saw them. The replicators came down the hall in swarms. SG-1 fired their weapons and the Spartans did the same. Cheney and his team tried, but their phaser rifles had no effect.

"Fall back" said Mitchell as he threw a frag grenade "Sam, call the _odyssey_".

* * *

The _Gettysburg's_ holo ship trick didn't fool the UNSC fleet for long and a recent hit had fried the emitters. Anderson had just gotten the message from the _odyssey_ about the prowlers.

"Commander, fire the isotope charge".

The _Gettysburg_ launched a modified quantum torpedo which streaked away and detonated between the ship and the UNSC fleet. It was designed to spread a certain isotope that gives off an energy signature if it comes into contact with a metallic substance. Namely, the hull of a prowler.

"Sir, I've got them" said Baker "5 ships on a direct course for us".

"Disable them" he ordered

"Aye, sir" but then the ship was rocked by another MAC slug. "Sir, shields have collapsed!"

The Gettysburg was hit by several archer missiles. The bridge began to shake, sparks were flying from consoles.

"Report?" Anderson cried as he griped his chair.

"Weapons and engines are down. Those prowlers have us dead to rights".

The captain thought they were done for, but then he saw the _odyssey_ heading for the prowlers.

--

"Keep us on course" said Keyes "and prepare for transport".

"Ma'am the prowlers are arming their nukes".

"Beam out the warhead"

The _odyssey_ dropped it shields for only a few seconds. Long enough though to beam one of their own nuclear warheads behind the prowlers. The _odyssey_ reestablished their shields and sped away just as a white light formed behind the prowlers.

"We did it!" said Keyes. Just then, Carter's frantic voice filled the bridge speakers

"_odyssey this is Carter. Don't ask how but the replicators are here. You need to transmit the shutdown code!" _

"Understood colonel we're …." She was cut off as the odyssey was rocked by an explosion. A HORNET mine drifted past the Odyssey's rail gun barrier and detonated right on their shields. This was followed by a MAC shredder slug which splintered as it made contact with the Odyssey's shields. Most of the shrapnel was deflected away but some got through and cut into the hull.

"Commander" said major marks "we've got multiple hull breaches, rail guns and beam weapons are down and we've lost the primary COM array. The backup is still functioning"

"Can we still transmit the signal?"

"Yes, but we need to be with in 5000 ft of the target" said marks.

"Then take us down".

"Ma'am what about the _Gettysburg_?"

Keyes had forgot about Anderson and his ship. She looked out at the stricken starfleet cruiser.

"Do we have any kind of single ship fighters aboard?" she asked

"Yes, 16 F-302s"

"Launch them then take us down"

The fighters left the hanger bays of the _odyssey_ and took up a defensive pattern around the crippled _Gettysburg._ Then the _odyssey_ began its decent into the atmosphere.

"Status?" asked Keyes. She could see the flames of reentry licking the shields of the _odyssey._

"Ma'am the decent thrusters just gave out. We can't slow down and according to these readings: if we don't change course before we hit 15,000 feet, we'll reach terminal velocity and we won't be able to break off!"

"Hold your course" she ordered.

* * *

On the bridge of the Valiant, Donna stood with the ship's commander, colonel Mace. She had been told by the Doctor to wait on board and keep an eye on the TARDIS, which thanks to the sacred jewel Kagome provided. Allowed the TARDIS the ability to travel between parallel universe, and to tow other objects with it.

"Sir" reported captain price "radar is picking up a large object entering the upper atmosphere. I don't believe it... its heading straight for us! Impact in less than two minutes!"

"Back us off" said the colonel.

"Wait, what about the Doctor?" said Donna

"We can't send anyone in to retrieve him. We need to get clear alert the ground forces to evacuate".

Donna could only watch as she saw the fireball heading for ONI HQ.

--

John and his group were cornered. They had gone down a hallway to a stairwell but the door was locked and the doctor was trying his sonic screwdriver on the keypad. The replicators were pouring down the hallway, sure John's team had infinite ammo, but there were too many of them and SG-1 had lost contact with the _odyssey_. John assumed the worst and knew what was coming. So he turned to Cortana and nodded at her as he removed a plasma grenade from his belt. Cortana saw this and nodded back, knowing what he was going to do.

--

"We're passing through 15,000 feet" screamed Marks. The bridge was ablaze in showers of sparks.

"Hold your course" said Keyes

"Shield failure in 90 seconds" reported the lieutenant to her left.

"Ma'am, we're passing through 10,000 ft impact in 30 seconds. 9000 ft…8… 7…6…We've hit 5,000!".

"Transmit!" said Keyes. She knew it was up to the engines now.

"3,000 ft…2,000, impact in 10 seconds!"

"Engage NOW!"

The _odyssey_ was about to hit the complex, but at the last second a hyperspace window opened up and the _odyssey_ went screaming into it. And then the window closed.

--

John was preparing to prime the grenade when all of a sudden. All the replicators began to fall apart.

"The shutdown code" said Carter.

"I've got it" said the Doctor who managed to get the stairwell door open. The Spartans went in first and proceeded up the stairs, John stopped the others from coming.

"We need to take care of this ourselves" he said. Before the others could object, he was already on his way upstairs to their objective, vice admiral Parangosky the head of ONI.

* * *

Anderson watched from the bridge as the small group of fighters took position in front of the _Gettysburg_.

"Captain, sensors indicate those fighters are not armed with much"

"I figured" he replied. The captain could see the fleet coming around and preparing to finish him off. He was about to order the crew to the escape pods when he herd Baker call out to him.

"Captain, 7 of those ships are moving toward us".

"_This is it"_ he thought to himself.

"Wait" said Baker "Captain, I don't believe it! They're taking up a defective position with the fighters!"

--

"What the hell are they doing?" said Adams from the bridge of his ship; he just saw what had happened.

"Sir, Cairo station is hailing the fleet"

"Put it on". One of the bridge monitors changed to hood's face

"_listen up"_ he began "_those ships are operating on my orders. What ONI didn't tell you it that they staged that attack and framed the Gettysburg to cover up their own raid on that ship. Anderson and his crew are good, honest people. They would never fire on us so if you want to follow ONI's half-assed orders then you'll have to go through our own ships first"._

"_He can't be serious"_ thought Adams.

"Sir, the fleet is disengaging".

"And we'll do the same" said Adams. _"I'm not about to start a civil war"_ he said to himself.

* * *

Vice admiral Parangosky was standing at her desk. Thanks to the _odyssey,_ the _valiant_ was scared away. A pelican was now inbound to evacuate her to a waiting prowler, then she would escape to the other colonies.

"They may have won the battle but the war is mine" she said as she got ready to leave. But the door was blown apart and the Spartans came in, pointing their guns at her. "Well don't you all have me surrounded" she said in a taunting tone.

"Its over, admiral" said john.

"Over, oh far from it"

Before they could react she hit a button on her desk The speakers in the Spartan's helmets began broadcasting a hypersonic tone and they lost conciseness.

--

"Chief, wake up!"

John regained conciseness. His helmet was off and he felt groggy. He looked around and saw the others had their helmets off as well. But Cortana's was lying on the ground and she was nowhere in sight, John immediately knew what had happened.

"They're heading for the roof. Go!" said Fred as he and Kelly tended to Linda who was still out of it.

John immediately scooped up his rifle, ran for the staircase and began heading for the roof. His shields wouldn't reactivate for some reason, probably caused by what ever Parangosky used. "I won't let that woman harm Cortana" he said to himself as he opened the door to the roof and ascended another staircase that led to a landing platform. Standing on the other end was Parangosky holding a pistol to Cortana's head.

"Drop it, or your girlfriend gets a new hole for another neural interface" she barked at the Chief.

John dropped his rifle.

"Thank you" she said as she pointed her gun at John and fired.

"NO!" Cortana screamed as the armor piercing round tore through John's armor and hit him in his lower chest. Blood began to flow out of the wound as he collapsed.

"And now it's your turn" Parangosky said as she pointed the gun at Cortana's head. But before she pulled the trigger a phaser beam struck Parangosky in her face and she screamed. Then Cortana elbowed her in the chest which caused Parangosky to drop her gun and stager back. Cortana looked to see who had fired and saw Cheney holding his phaser.

"YOU SHOT ME IN THE FACE!" she screamed at him

"Did I" he said as he shot the admiral in the chest on the stun setting. Cortana rushed over to John's side with tears in her eyes. John was already sitting up when she reached him and she grabbed him in a tight embrace.

"I thought you were dead" she said.

"Its ok" he replied "it's over".


	14. epilogue

**Disclaimer: I don't own halo or any other TV show or book mentioned in this story**

**Epilogue: goodbyes **

It was a bittersweet moment on the bridge of the Cairo. On the main display was the bridge of the _Gettysburg._ Captain Anderson was standing with the rest of his senior staff, looking at the group of people on the bridge of the Cairo. John and the rest of blue team in their dress uniforms. Along with hood, the Arbiter and Keyes.

"_Its finally over"_ John thought to himself. Vice admiral Parangosky was being court-martialed for treason. She confessed to orchestrating the whole affair but they knew she was protecting others who were involved. The Doctor had been successful in using the TARDIS to send the _valiant_ back to his universe and the _odyssey_ to their own. Now it was the _Gettysburg's_ turn.

"_Gentlemen it's been an honor"_ said Anderson.

"The honor was ours" said hood "the UNSC owes you and your crew a debt of gratitude for your actions".

"_Thank you admiral. And Chief, take care of yourself and your team"_

"I will, captain" said John.

"_Anderson out"_ then the screen switched back to the UNSC logo.

* * *

"Ready to go home?" said Anderson as his crew was taking their stations

"Yes, sir" they all said.

"Good" he said as the captain took his own seat

--

The Doctor was standing in the TARDIS with Donna, Kagome and Inuyasha. He'd parked the TARDIS in engineering so they could hook the ship up.

"Is there any chance I can persuade you two to let me hang on to that jewel of yours?" said the Doctor "I would love to check out some of the parallel universes that are out there"

"Sorry Doctor, But I have plans for that jewel" said Inuyasha.

"We, have plans!" said Kagome

The Doctor finished hooking up the last wires from the center console that led out of the TARDIS, and into a panel in front of the warp core in engineering. Collins was amazed as he walked into the TARDIS and gawked at its size on the inside

"are we ready, Doctor?" he asked.

"Yep, just finished" as he connected the last wire.

"_Anderson to engineering, lets go home."_

"Aye, sir" said Collins as the Doctor threw a switch on the TARDIS.

* * *

John watched from the Cairo Bridge as the _Gettysburg_ shimmered away.

"I'm going to miss them" said Cortana who was standing next to him in her new dress uniform. Hood had given her a commission with the rank of petty officer second class.

"I know" he replied "but for now we need to celebrate your promotion".

"I agree" said Kelly.

"Same here" said Lucy.

"Ok, then lets go" said Cortana and with that blue team left the bridge and headed for the commissary.

Tarinus summoned his second-in-command to the prophet's chamber, to share with him what he learned from the prophet's private databanks.

"Tarinus" he said as he entered "what have you learned?"

"I believe I have found a way to defeat the humans and their heretics once and for all. We must seek out this ancient enemy the forerunners mentioned in the sacred text".

"You speak of the flood" said his XO sounding puzzled

"No, the prophet's texts speak in great detail of this older enemy the forerunners fought before the flood. And I believe they are still here. With their help, we will defeat the humans and expand our great new covenant across the galaxy".

**Message from the general: **well I hope you enjoyed this story as much as I did writing it and I'm planning on a sequel but it won't be out until after my next story but check my profile for updates


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